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Cipriano A, Colantoni A, Calicchio A, Fiorentino J, Gomes D, Moqri M, Parker A, Rasouli S, Caldwell M, Briganti F, Roncarolo MG, Baldini A, Weinacht KG, Tartaglia GG, Sebastiano V. Transcriptional and epigenetic characterization of a new in vitro platform to model the formation of human pharyngeal endoderm. Genome Biol 2024; 25:211. [PMID: 39118163 PMCID: PMC11312149 DOI: 10.1186/s13059-024-03354-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 07/26/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND The Pharyngeal Endoderm (PE) is an extremely relevant developmental tissue, serving as the progenitor for the esophagus, parathyroids, thyroids, lungs, and thymus. While several studies have highlighted the importance of PE cells, a detailed transcriptional and epigenetic characterization of this important developmental stage is still missing, especially in humans, due to technical and ethical constraints pertaining to its early formation. RESULTS Here we fill this knowledge gap by developing an in vitro protocol for the derivation of PE-like cells from human Embryonic Stem Cells (hESCs) and by providing an integrated multi-omics characterization. Our PE-like cells robustly express PE markers and are transcriptionally homogenous and similar to in vivo mouse PE cells. In addition, we define their epigenetic landscape and dynamic changes in response to Retinoic Acid by combining ATAC-Seq and ChIP-Seq of histone modifications. The integration of multiple high-throughput datasets leads to the identification of new putative regulatory regions and to the inference of a Retinoic Acid-centered transcription factor network orchestrating the development of PE-like cells. CONCLUSIONS By combining hESCs differentiation with computational genomics, our work reveals the epigenetic dynamics that occur during human PE differentiation, providing a solid resource and foundation for research focused on the development of PE derivatives and the modeling of their developmental defects in genetic syndromes.
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Affiliation(s)
- Andrea Cipriano
- Department of Obstetrics & Gynecology, Stanford University, Stanford, CA, 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine (ISCBRM), Stanford School of Medicine, Stanford, CA, 94305, USA
| | - Alessio Colantoni
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, 00185, Rome, Italy
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano Di Tecnologia (IIT), 00161, Rome, Italy
| | - Alessandro Calicchio
- Department of Obstetrics & Gynecology, Stanford University, Stanford, CA, 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine (ISCBRM), Stanford School of Medicine, Stanford, CA, 94305, USA
| | - Jonathan Fiorentino
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano Di Tecnologia (IIT), 00161, Rome, Italy
| | - Danielle Gomes
- Department of Obstetrics & Gynecology, Stanford University, Stanford, CA, 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine (ISCBRM), Stanford School of Medicine, Stanford, CA, 94305, USA
| | - Mahdi Moqri
- Biomedical Informatics Program, Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Alexander Parker
- Department of Obstetrics & Gynecology, Stanford University, Stanford, CA, 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine (ISCBRM), Stanford School of Medicine, Stanford, CA, 94305, USA
| | - Sajede Rasouli
- Department of Obstetrics & Gynecology, Stanford University, Stanford, CA, 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine (ISCBRM), Stanford School of Medicine, Stanford, CA, 94305, USA
| | - Matthew Caldwell
- Department of Obstetrics & Gynecology, Stanford University, Stanford, CA, 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine (ISCBRM), Stanford School of Medicine, Stanford, CA, 94305, USA
| | - Francesca Briganti
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, 94305, USA
- Cardiovascular Institute and Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Maria Grazia Roncarolo
- Institute for Stem Cell Biology and Regenerative Medicine (ISCBRM), Stanford School of Medicine, Stanford, CA, 94305, USA
- Division of Hematology, Oncology, Stem Cell Transplantation, and Regenerative Medicine, Department of Pediatrics, Stanford School of Medicine, Stanford, CA, 94305, USA
- Center for Definitive and Curative Medicine (CDCM), Stanford School of Medicine, Stanford, CA, USA
| | - Antonio Baldini
- Department of Molecular Medicine and Medical Biotech., University Federico II, 80131, Naples, Italy
| | - Katja G Weinacht
- Division of Hematology, Oncology, Stem Cell Transplantation, and Regenerative Medicine, Department of Pediatrics, Stanford School of Medicine, Stanford, CA, 94305, USA
| | - Gian Gaetano Tartaglia
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano Di Tecnologia (IIT), 00161, Rome, Italy.
- Center for Human Technology, Fondazione Istituto Italiano Di Tecnologia (IIT), 16152, Genoa, Italy.
| | - Vittorio Sebastiano
- Department of Obstetrics & Gynecology, Stanford University, Stanford, CA, 94305, USA.
- Institute for Stem Cell Biology and Regenerative Medicine (ISCBRM), Stanford School of Medicine, Stanford, CA, 94305, USA.
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Psutkova V, Nickl P, Brezinova V, Machonova O, Machon O. Transcription factor Meis1b regulates craniofacial morphogenesis in zebrafish. Dev Dyn 2024. [PMID: 39087648 DOI: 10.1002/dvdy.731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 06/28/2024] [Accepted: 07/17/2024] [Indexed: 08/02/2024] Open
Abstract
BACKGROUND Meis family of transcription factors operates in Pbx-Meis-Hox regulatory network controlling development of various tissues including eye, limbs, heart, hindbrain or craniofacial skeletal elements originating from the neural crest. Although studies in mouse provide abundant information about Meis factors function in embryogenesis, little is known about their role in zebrafish. RESULTS We generated zebrafish lines carrying null mutations in meis1a, meis1b, meis2a, and meis2b genes. Only meis1b mutants are lethal at larval stage around 13 dpf whereas the other mutant lines are viable and fertile. We focused on development of neural crest-derived craniofacial structures such as tendons, cranial nerves, cartilage and accompanying muscles. Meis1b mutants displayed morphogenetic abnormalities in the cartilage originating from the first and second pharyngeal arches. Meckel's cartilage was shorter and wider with fused anterior symphysis and abnormal chondrocyte organization. This resulted in impaired tendons and muscle fiber connections while tenocyte development was not largely affected. CONCLUSIONS Loss-of-function mutation in meis1b affects cartilage morphology in the lower jaw that leads to disrupted organization of muscles and tendons.
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Affiliation(s)
- Viktorie Psutkova
- Department of Developmental Biology, Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Petr Nickl
- Department of Developmental Biology, Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czech Republic
| | - Veronika Brezinova
- Department of Developmental Biology, Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czech Republic
| | - Olga Machonova
- Laboratory of Cell Differentiation, Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Ondrej Machon
- Department of Developmental Biology, Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czech Republic
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3
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de Sena-Tomás C, Rebola Lameira L, Rebocho da Costa M, Naique Taborda P, Laborde A, Orger M, de Oliveira S, Saúde L. Neutrophil immune profile guides spinal cord regeneration in zebrafish. Brain Behav Immun 2024; 120:514-531. [PMID: 38925414 DOI: 10.1016/j.bbi.2024.06.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 05/15/2024] [Accepted: 06/23/2024] [Indexed: 06/28/2024] Open
Abstract
Spinal cord injury triggers a strong innate inflammatory response in both non-regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet, their role in the repair process, particularly in a regenerative context, remains largely unknown. Here, we show that, following rapid recruitment to the injured spinal cord, neutrophils mostly reverse migrate throughout the zebrafish body. In addition, promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil-specific RNA-seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf-α expression in macrophage/microglia populations. Conversely, blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether, these findings provide new insights into the role of neutrophils in spinal cord regeneration, emphasizing the significant impact of their immune profile on the outcome of the repair process.
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Affiliation(s)
- Carmen de Sena-Tomás
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal.
| | - Leonor Rebola Lameira
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Mariana Rebocho da Costa
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Patrícia Naique Taborda
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Alexandre Laborde
- Champalimaud Research, Champalimaud Centre for the Unknown, 1400-038 Lisboa, Portugal
| | - Michael Orger
- Champalimaud Research, Champalimaud Centre for the Unknown, 1400-038 Lisboa, Portugal
| | - Sofia de Oliveira
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Medicine (Hepatology), Albert Einstein College of Medicine, Bronx, NY 10461, USA; Harold and Muriel Block Institute for Clinical and Translational Research, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Montefiore-Einstein Comprehensive Cancer Research Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Leonor Saúde
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal; Instituto de Histologia e Biologia de Desenvolvimento, Faculdade de Medicina da Universidade de Lisboa, 1649-028 Lisboa, Portugal.
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4
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Erdem M, Lee KH, Hardt M, Regan JL, Kobelt D, Walther W, Mokrizkij M, Regenbrecht C, Stein U. MACC1 Regulates LGR5 to Promote Cancer Stem Cell Properties in Colorectal Cancer. Cancers (Basel) 2024; 16:604. [PMID: 38339354 PMCID: PMC10854991 DOI: 10.3390/cancers16030604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 01/18/2024] [Accepted: 01/20/2024] [Indexed: 02/12/2024] Open
Abstract
Colorectal cancer (CRC) is one of the leading causes of cancer-related deaths worldwide. The high mortality is directly associated with metastatic disease, which is thought to be initiated by colon cancer stem cells, according to the cancer stem cell (CSC) model. Consequently, early identification of those patients who are at high risk for metastasis is crucial for improved treatment and patient outcomes. Metastasis-associated in colon cancer 1 (MACC1) is a novel prognostic biomarker for tumor progression and metastasis formation independent of tumor stage. We previously showed an involvement of MACC1 in cancer stemness in the mouse intestine of our MACC1 transgenic mouse models. However, the expression of MACC1 in human CSCs and possible implications remain elusive. Here, we explored the molecular mechanisms by which MACC1 regulates stemness and the CSC-associated invasive phenotype based on patient-derived tumor organoids (PDOs), patient-derived xenografts (PDXs) and human CRC cell lines. We showed that CD44-enriched CSCs from PDO models express significantly higher levels of MACC1 and LGR5 and display higher tumorigenicity in immunocompromised mice. Similarly, RNA sequencing performed on PDO and PDX models demonstrated significantly increased MACC1 expression in ALDH1(+) CSCs, highlighting its involvement in cancer stemness. We further showed the correlation of MACC1 with the CSC markers CD44, NANOG and LGR5 in PDO models as well as established cell lines. Additionally, MACC1 increased stem cell gene expression, clonogenicity and sphere formation. Strikingly, we showed that MACC1 binds as a transcription factor to the LGR5 gene promoter, uncovering the long-known CSC marker LGR5 as a novel essential signaling mediator employed by MACC1 to induce CSC-like properties in human CRC patients. Our in vitro findings were further substantiated by a significant positive correlation of MACC1 with LGR5 in CRC cell lines as well as CRC patient tumors. Taken together, this study indicates that the metastasis inducer MACC1 acts as a cancer stem cell-associated marker. Interventional approaches targeting MACC1 would potentially improve further targeted therapies for colorectal cancer patients to eradicate CSCs and prevent cancer recurrence and distant metastasis formation.
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Affiliation(s)
- Müge Erdem
- Experimental and Clinical Research Center, Charité—Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Translational Oncology of Solid Tumors Research Group, 13125 Berlin, Germany (D.K.)
| | - Kyung Hwan Lee
- Experimental and Clinical Research Center, Charité—Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Translational Oncology of Solid Tumors Research Group, 13125 Berlin, Germany (D.K.)
| | - Markus Hardt
- Experimental and Clinical Research Center, Charité—Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Translational Oncology of Solid Tumors Research Group, 13125 Berlin, Germany (D.K.)
| | - Joseph L. Regan
- Bayer AG, Research and Development, Pharmaceuticals, 13342 Berlin, Germany
- JLR Life Sciences Ltd., A96 A8D5 Dublin, Ireland
| | - Dennis Kobelt
- Experimental and Clinical Research Center, Charité—Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Translational Oncology of Solid Tumors Research Group, 13125 Berlin, Germany (D.K.)
- German Cancer Consortium, 69120 Heidelberg, Germany
| | - Wolfgang Walther
- Experimental and Clinical Research Center, Charité—Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Translational Oncology of Solid Tumors Research Group, 13125 Berlin, Germany (D.K.)
| | - Margarita Mokrizkij
- Experimental and Clinical Research Center, Charité—Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Translational Oncology of Solid Tumors Research Group, 13125 Berlin, Germany (D.K.)
| | | | - Ulrike Stein
- Experimental and Clinical Research Center, Charité—Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Translational Oncology of Solid Tumors Research Group, 13125 Berlin, Germany (D.K.)
- German Cancer Consortium, 69120 Heidelberg, Germany
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Agostini V, Tessier A, Djaziri N, Khonsari RH, Galliani E, Kurihara Y, Honda M, Kurihara H, Hidaka K, Tuncbilek G, Picard A, Konas E, Amiel J, Gordon CT. Biallelic truncating variants in VGLL2 cause syngnathia in humans. J Med Genet 2023; 60:1084-1091. [PMID: 37666660 DOI: 10.1136/jmg-2022-109059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 04/24/2023] [Indexed: 09/06/2023]
Abstract
BACKGROUND Syngnathia is an ultrarare craniofacial malformation characterised by an inability to open the mouth due to congenital fusion of the upper and lower jaws. The genetic causes of isolated bony syngnathia are unknown. METHODS We used whole exome and Sanger sequencing and microsatellite analysis in six patients (from four families) presenting with syngnathia. We used CRISPR/Cas9 genome editing to generate vgll2a and vgll4l germline mutant zebrafish, and performed craniofacial cartilage analysis in homozygous mutants. RESULTS We identified homozygous truncating variants in vestigial-like family member 2 (VGLL2) in all six patients. Two alleles were identified: one in families of Turkish origin and the other in families of Moroccan origin, suggesting a founder effect for each. A shared haplotype was confirmed for the Turkish patients. The VGLL family of genes encode cofactors of TEAD transcriptional regulators. Vgll2 is regionally expressed in the pharyngeal arches of model vertebrate embryos, and morpholino-based knockdown of vgll2a in zebrafish has been reported to cause defects in development of pharyngeal arch cartilages. However, we did not observe craniofacial anomalies in vgll2a or vgll4l homozygous mutant zebrafish nor in fish with double knockout of vgll2a and vgll4l. In Vgll2 -/- mice, which are known to present a skeletal muscle phenotype, we did not identify defects of the craniofacial skeleton. CONCLUSION Our results suggest that although loss of VGLL2 leads to a striking jaw phenotype in humans, other vertebrates may have the capacity to compensate for its absence during craniofacial development.
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Affiliation(s)
- Valeria Agostini
- Laboratory of embryology and genetics of human malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine and Université Paris Cité, Paris, France
| | - Aude Tessier
- Laboratory of embryology and genetics of human malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine and Université Paris Cité, Paris, France
| | - Nabila Djaziri
- Laboratory of embryology and genetics of human malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine and Université Paris Cité, Paris, France
| | - Roman Hossein Khonsari
- Service de Chirurgie Maxillofaciale et Chirurgie Plastique, Centre de référence Fentes et Malformations Faciales (MAFACE), Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris Cité, Paris, France
| | - Eva Galliani
- Service de Chirurgie Maxillofaciale et Chirurgie Plastique, Centre de référence Fentes et Malformations Faciales (MAFACE), Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris Cité, Paris, France
| | - Yukiko Kurihara
- Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masahiko Honda
- Department of Biochemistry, Faculty of Medicine, Kindai University, Osaka-Sayama, Japan
| | - Hiroki Kurihara
- Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kyoko Hidaka
- Department of Bioscience and Genetics, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan
| | | | - Arnaud Picard
- Service de Chirurgie Maxillofaciale et Chirurgie Plastique, Centre de référence Fentes et Malformations Faciales (MAFACE), Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris Cité, Paris, France
| | | | - Jeanne Amiel
- Laboratory of embryology and genetics of human malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine and Université Paris Cité, Paris, France
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Christopher T Gordon
- Laboratory of embryology and genetics of human malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine and Université Paris Cité, Paris, France
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Yamada M, Tanito K, Suzuki H, Nakato D, Miya F, Takenouchi T, Kosaki K. Café-au-lait Spots and Cleft Palate: Not a Chance Association. Cleft Palate Craniofac J 2023:10556656231188205. [PMID: 37448313 DOI: 10.1177/10556656231188205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/15/2023] Open
Abstract
The recognition of syndromic forms of cleft palate is important for condition-specific management. Here, we report a patient with cleft palate, congenital heart disease, intellectual disability, and café-au-lait spots who had a deletion of chromosome 15q14. The identification of the precise breakpoints using a Nanopore-based long-read sequencer showed that the deletion spanned MEIS2 and SPRED1 loci. Cleft palate and café-au-lait spots can be ascribed to MEIS2 and SPRED1, respectively. Patients with cleft palate and café-au-lait spots should be encouraged to undergo a detailed genomic evaluation, including screening for a 15q14 deletion, to enable appropriate anticipatory medico-surgical management and genetic counseling.
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Affiliation(s)
- Mamiko Yamada
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | | | - Hisato Suzuki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Daisuke Nakato
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Fuyuki Miya
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Toshiki Takenouchi
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
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7
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Wu Z, Yang KG, Lam TP, Cheng JCY, Zhu Z, Lee WYW. Genetic insight into the putative causal proteins and druggable targets of osteoporosis: a large-scale proteome-wide mendelian randomization study. Front Genet 2023; 14:1161817. [PMID: 37448626 PMCID: PMC10336211 DOI: 10.3389/fgene.2023.1161817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 06/12/2023] [Indexed: 07/15/2023] Open
Abstract
Background: Osteoporosis is a major causative factor of the global burden of disease and disability, characterized by low bone mineral density (BMD) and high risks of fracture. We aimed to identify putative causal proteins and druggable targets of osteoporosis. Methods: This study utilized the largest GWAS summary statistics on plasma proteins and estimated heel BMD (eBMD) to identify causal proteins of osteoporosis by mendelian randomization (MR) analysis. Different GWAS datasets were used to validate the results. Multiple sensitivity analyses were conducted to evaluate the robustness of primary MR findings. We have also performed an enrichment analysis for the identified causal proteins and evaluated their druggability. Results: After Bonferroni correction, 67 proteins were identified to be causally associated with estimated BMD (eBMD) (p < 4 × 10-5). We further replicated 38 of the 67 proteins to be associated with total body BMD, lumbar spine BMD, femoral neck BMD as well as fractures, such as RSPO3, IDUA, SMOC2, and LRP4. The findings were supported by sensitivity analyses. Enrichment analysis identified multiple Gene Ontology items, including collagen-containing extracellular matrix (GO:0062023, p = 1.6 × 10-10), collagen binding (GO:0005518, p = 8.6 × 10-5), and extracellular matrix structural constituent (GO:0005201, p = 2.7 × 10-5). Conclusion: The study identified novel putative causal proteins for osteoporosis which may serve as potential early screening biomarkers and druggable targets. Furthermore, the role of plasma proteins involved in collagen binding and extracellular matrix in the development of osteoporosis was highlighted. Further studies are warranted to validate our findings and investigate the underlying mechanism.
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Affiliation(s)
- Zhichong Wu
- Division of Spine Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
- Musculoskeletal Research Laboratory, SH Ho Scoliosis Research Laboratory, Department of Orthopaedics and Traumatology, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Joint Scoliosis Research Centre of the Chinese University of Hong Kong and Nanjing University, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Kenneth Guangpu Yang
- Musculoskeletal Research Laboratory, SH Ho Scoliosis Research Laboratory, Department of Orthopaedics and Traumatology, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Joint Scoliosis Research Centre of the Chinese University of Hong Kong and Nanjing University, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Prince of Wales Hospital, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Center for Neuromusculoskeletal Restorative Medicine, CUHK InnoHK Centres, Shatin, Hong Kong SAR, China
- Key Laboratory for Regenerative Medicine, School of Biomedical Sciences, Faculty of Medicine, Ministry of Education, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Tsz-Ping Lam
- Joint Scoliosis Research Centre of the Chinese University of Hong Kong and Nanjing University, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Jack Chun Yiu Cheng
- Joint Scoliosis Research Centre of the Chinese University of Hong Kong and Nanjing University, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Zezhang Zhu
- Division of Spine Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
- Musculoskeletal Research Laboratory, SH Ho Scoliosis Research Laboratory, Department of Orthopaedics and Traumatology, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Joint Scoliosis Research Centre of the Chinese University of Hong Kong and Nanjing University, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Wayne Yuk-Wai Lee
- Musculoskeletal Research Laboratory, SH Ho Scoliosis Research Laboratory, Department of Orthopaedics and Traumatology, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Joint Scoliosis Research Centre of the Chinese University of Hong Kong and Nanjing University, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Prince of Wales Hospital, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Center for Neuromusculoskeletal Restorative Medicine, CUHK InnoHK Centres, Shatin, Hong Kong SAR, China
- Key Laboratory for Regenerative Medicine, School of Biomedical Sciences, Faculty of Medicine, Ministry of Education, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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Zieger HK, Weinhold L, Schmidt A, Holtgrewe M, Juranek SA, Siewert A, Scheer AB, Thieme F, Mangold E, Ishorst N, Brand FU, Welzenbach J, Beule D, Paeschke K, Krawitz PM, Ludwig KU. Prioritization of non-coding elements involved in non-syndromic cleft lip with/without cleft palate through genome-wide analysis of de novo mutations. HGG ADVANCES 2022; 4:100166. [PMID: 36589413 PMCID: PMC9795529 DOI: 10.1016/j.xhgg.2022.100166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Non-syndromic cleft lip with/without cleft palate (nsCL/P) is a highly heritable facial disorder. To date, systematic investigations of the contribution of rare variants in non-coding regions to nsCL/P etiology are sparse. Here, we re-analyzed available whole-genome sequence (WGS) data from 211 European case-parent trios with nsCL/P and identified 13,522 de novo mutations (DNMs) in nsCL/P cases, 13,055 of which mapped to non-coding regions. We integrated these data with DNMs from a reference cohort, with results of previous genome-wide association studies (GWASs), and functional and epigenetic datasets of relevance to embryonic facial development. A significant enrichment of nsCL/P DNMs was observed at two GWAS risk loci (4q28.1 (p = 8 × 10-4) and 2p21 (p = 0.02)), suggesting a convergence of both common and rare variants at these loci. We also mapped the DNMs to 810 position weight matrices indicative of transcription factor (TF) binding, and quantified the effect of the allelic changes in silico. This revealed a nominally significant overrepresentation of DNMs (p = 0.037), and a stronger effect on binding strength, for DNMs located in the sequence of the core binding region of the TF Musculin (MSC). Notably, MSC is involved in facial muscle development, together with a set of nsCL/P genes located at GWAS loci. Supported by additional results from single-cell transcriptomic data and molecular binding assays, this suggests that variation in MSC binding sites contributes to nsCL/P etiology. Our study describes a set of approaches that can be applied to increase the added value of WGS data.
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Affiliation(s)
- Hanna K. Zieger
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
| | - Leonie Weinhold
- Institute for Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn 53127, Germany
| | - Axel Schmidt
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
| | - Manuel Holtgrewe
- Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany
| | - Stefan A. Juranek
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn 53127, Germany
| | - Anna Siewert
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
| | - Annika B. Scheer
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
| | - Frederic Thieme
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
| | - Elisabeth Mangold
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
| | - Nina Ishorst
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
| | - Fabian U. Brand
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn 53127, Germany
| | - Julia Welzenbach
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
| | - Dieter Beule
- Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany,Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
| | - Katrin Paeschke
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn 53127, Germany
| | - Peter M. Krawitz
- Institute for Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn 53127, Germany
| | - Kerstin U. Ludwig
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany,Corresponding author
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9
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Leyhr J, Waldmann L, Filipek-Górniok B, Zhang H, Allalou A, Haitina T. A novel cis-regulatory element drives early expression of Nkx3.2 in the gnathostome primary jaw joint. eLife 2022; 11:75749. [PMCID: PMC9665848 DOI: 10.7554/elife.75749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 09/30/2022] [Indexed: 11/16/2022] Open
Abstract
The acquisition of movable jaws was a major event during vertebrate evolution. The role of NK3 homeobox 2 (Nkx3.2) transcription factor in patterning the primary jaw joint of gnathostomes (jawed vertebrates) is well known, however knowledge about its regulatory mechanism is lacking. In this study, we report a proximal enhancer element of Nkx3.2 that is deeply conserved in most gnathostomes but undetectable in the jawless hagfish and lamprey. This enhancer is active in the developing jaw joint region of the zebrafish Danio rerio, and was thus designated as jaw joint regulatory sequence 1 (JRS1). We further show that JRS1 enhancer sequences from a range of gnathostome species, including a chondrichthyan and mammals, have the same activity in the jaw joint as the native zebrafish enhancer, indicating a high degree of functional conservation despite the divergence of cartilaginous and bony fish lineages or the transition of the primary jaw joint into the middle ear of mammals. Finally, we show that deletion of JRS1 from the zebrafish genome using CRISPR/Cas9 results in a significant reduction of early gene expression of nkx3.2 and leads to a transient jaw joint deformation and partial fusion. Emergence of this Nkx3.2 enhancer in early gnathostomes may have contributed to the origin and shaping of the articulating surfaces of vertebrate jaws.
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Affiliation(s)
- Jake Leyhr
- Subdepartment of Evolution and Development, Department of Organismal Biology, Uppsala University
| | - Laura Waldmann
- Subdepartment of Evolution and Development, Department of Organismal Biology, Uppsala University
| | - Beata Filipek-Górniok
- Science for Life Laboratory Genome Engineering Zebrafish Facility, Department of Organismal Biology, Uppsala University
| | - Hanqing Zhang
- Division of Visual Information and Interaction, Department of Information Technology, Uppsala University
- Science for Life Laboratory BioImage Informatics Facility
| | - Amin Allalou
- Division of Visual Information and Interaction, Department of Information Technology, Uppsala University
- Science for Life Laboratory BioImage Informatics Facility
| | - Tatjana Haitina
- Subdepartment of Evolution and Development, Department of Organismal Biology, Uppsala University
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10
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Maridas DE, Gamer L, Moore ER, Doedens AM, Yu Y, Ionescu A, Revollo L, Whitman M, Rosen V. Loss of Vlk in Prx1 + Cells Delays the Initial Steps of Endochondral Bone Formation and Fracture Repair in the Limb. J Bone Miner Res 2022; 37:764-775. [PMID: 35080046 DOI: 10.1002/jbmr.4514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 12/29/2021] [Accepted: 01/21/2022] [Indexed: 11/10/2022]
Abstract
Vertebrate lonesome kinase (Vlk) is a secreted tyrosine kinase important for normal skeletogenesis during embryonic development. Vlk null mice (Vlk-/- ) are born with severe craniofacial and limb skeletal defects and die shortly after birth. We used a conditional deletion model to remove Vlk in limb bud mesenchyme (Vlk-Prx1 cKO) to assess the specific requirement for Vlk expression by skeletal progenitor cells during endochondral ossification, and an inducible global deletion model (Vlk-Ubq iKO) to address the role of Vlk during fracture repair. Deletion of Vlk with Prx1-Cre recapitulated the limb skeletal phenotype of the Vlk-/- mice and enabled us to study the postnatal skeleton as Vlk-Prx1 cKO mice survived to adulthood. In Vlk-Prx1 cKO adult mice, limbs remained shorter with decreased trabecular and cortical bone volumes. Both Vlk-Prx1 cKO and Vlk-Ubq iKO mice had a delayed fracture repair response but eventually formed bridging calluses. Furthermore, levels of phosphorylated osteopontin (OPN) were decreased in tibias of Vlk-Ubq iKO, establishing OPN as a Vlk substrate in bone. In summary, our data indicate that Vlk produced by skeletal progenitor cells influences the timing and extent of chondrogenesis during endochondral bone formation and fracture repair. © 2022 American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- David E Maridas
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA, USA
| | - Laura Gamer
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA, USA
| | - Emily R Moore
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA, USA
| | - Annemiek M Doedens
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA, USA
| | - Yunqing Yu
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA, USA
| | | | - Leila Revollo
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA, USA
| | - Malcolm Whitman
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA, USA
| | - Vicki Rosen
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA, USA
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11
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Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis. Nat Commun 2021; 12:6094. [PMID: 34667153 PMCID: PMC8526749 DOI: 10.1038/s41467-021-26234-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 09/14/2021] [Indexed: 11/09/2022] Open
Abstract
Zygotic genome activation (ZGA) initiates regionalized transcription underlying distinct cellular identities. ZGA is dependent upon dynamic chromatin architecture sculpted by conserved DNA-binding proteins. However, the direct mechanistic link between the onset of ZGA and the tissue-specific transcription remains unclear. Here, we have addressed the involvement of chromatin organizer Satb2 in orchestrating both processes during zebrafish embryogenesis. Integrative analysis of transcriptome, genome-wide occupancy and chromatin accessibility reveals contrasting molecular activities of maternally deposited and zygotically synthesized Satb2. Maternal Satb2 prevents premature transcription of zygotic genes by influencing the interplay between the pluripotency factors. By contrast, zygotic Satb2 activates transcription of the same group of genes during neural crest development and organogenesis. Thus, our comparative analysis of maternal versus zygotic function of Satb2 underscores how these antithetical activities are temporally coordinated and functionally implemented highlighting the evolutionary implications of the biphasic and bimodal regulation of landmark developmental transitions by a single determinant. Activation of the zygotic genome is a critical transition during development, though the link to tissue-specific gene regulation remains unclear. Here the authors demonstrate distinct functions for Satb2 before and after zygotic genome activation, highlighting the temporal coordination of these roles.
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12
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Yang X, Cao N, Chen L, Liu L, Zhang M, Cao Y. Suppression of Cell Tumorigenicity by Non-neural Pro-differentiation Factors via Inhibition of Neural Property in Tumorigenic Cells. Front Cell Dev Biol 2021; 9:714383. [PMID: 34595169 PMCID: PMC8476888 DOI: 10.3389/fcell.2021.714383] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 08/16/2021] [Indexed: 11/13/2022] Open
Abstract
Our studies have demonstrated that cell tumorigenicity and pluripotent differentiation potential stem from neural stemness or a neural ground state, which is defined by a regulatory network of higher levels of machineries for basic cell physiological functions, including cell cycle, ribosome biogenesis, protein translation, spliceosome, epigenetic modification factors, reprogramming factors, etc., in addition to the neural stemness specific factors. These machineries and neural stemness factors mostly play cancer-promoting roles. It can be deduced that differentiation requires the repression of neural ground state and causes the reduction or loss of neural ground state and thus tumorigenicity in tumorigenic cells. Formerly, we showed that neuronal differentiation led to reduced tumorigenicity in tumorigenic cells. In the present study, we show that non-neural pro-differentiation factors, such as GATA3, HNF4A, HHEX, and FOXA3 that specify mesodermal or/and endodermal tissues during vertebrate embryogenesis, suppress tumorigenicity via repression of neural stemness and promotion of non-neural property in tumorigenic cells. Mechanistically, these transcription factors repress the transcription of neural enriched genes and meanwhile activate genes that specify non-neural properties via direct binding to the promoters of these genes. We also show that combined expression of HHEX and FOXA3 suppresses tumorigenesis effectively in the AOM/DSS model of colitis-associated cancer. We suggest that targeting the property of neural stemness could be an effective strategy for cancer therapy.
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Affiliation(s)
- Xiaoli Yang
- Shenzhen Research Institute of Nanjing University, Shenzhen, China
- MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
- Jiangsu Key Laboratory of Molecular Medicine of Medical School, Nanjing University, Nanjing, China
| | - Ning Cao
- Shenzhen Research Institute of Nanjing University, Shenzhen, China
- MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
- Jiangsu Key Laboratory of Molecular Medicine of Medical School, Nanjing University, Nanjing, China
| | - Lu Chen
- Shenzhen Research Institute of Nanjing University, Shenzhen, China
- MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
- Jiangsu Key Laboratory of Molecular Medicine of Medical School, Nanjing University, Nanjing, China
| | - Lin Liu
- MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
- Jiangsu Key Laboratory of Molecular Medicine of Medical School, Nanjing University, Nanjing, China
| | - Min Zhang
- Shenzhen Research Institute of Nanjing University, Shenzhen, China
- MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
- Jiangsu Key Laboratory of Molecular Medicine of Medical School, Nanjing University, Nanjing, China
| | - Ying Cao
- Shenzhen Research Institute of Nanjing University, Shenzhen, China
- MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
- Jiangsu Key Laboratory of Molecular Medicine of Medical School, Nanjing University, Nanjing, China
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13
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Fabik J, Psutkova V, Machon O. The Mandibular and Hyoid Arches-From Molecular Patterning to Shaping Bone and Cartilage. Int J Mol Sci 2021; 22:7529. [PMID: 34299147 PMCID: PMC8303155 DOI: 10.3390/ijms22147529] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/02/2021] [Accepted: 07/05/2021] [Indexed: 12/16/2022] Open
Abstract
The mandibular and hyoid arches collectively make up the facial skeleton, also known as the viscerocranium. Although all three germ layers come together to assemble the pharyngeal arches, the majority of tissue within viscerocranial skeletal components differentiates from the neural crest. Since nearly one third of all birth defects in humans affect the craniofacial region, it is important to understand how signalling pathways and transcription factors govern the embryogenesis and skeletogenesis of the viscerocranium. This review focuses on mouse and zebrafish models of craniofacial development. We highlight gene regulatory networks directing the patterning and osteochondrogenesis of the mandibular and hyoid arches that are actually conserved among all gnathostomes. The first part of this review describes the anatomy and development of mandibular and hyoid arches in both species. The second part analyses cell signalling and transcription factors that ensure the specificity of individual structures along the anatomical axes. The third part discusses the genes and molecules that control the formation of bone and cartilage within mandibular and hyoid arches and how dysregulation of molecular signalling influences the development of skeletal components of the viscerocranium. In conclusion, we notice that mandibular malformations in humans and mice often co-occur with hyoid malformations and pinpoint the similar molecular machinery controlling the development of mandibular and hyoid arches.
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Affiliation(s)
- Jaroslav Fabik
- Department of Developmental Biology, Institute of Experimental Medicine of the Czech Academy of Sciences, 14220 Prague, Czech Republic; (J.F.); (V.P.)
- Department of Cell Biology, Faculty of Science, Charles University, 12800 Prague, Czech Republic
| | - Viktorie Psutkova
- Department of Developmental Biology, Institute of Experimental Medicine of the Czech Academy of Sciences, 14220 Prague, Czech Republic; (J.F.); (V.P.)
- Department of Cell Biology, Faculty of Science, Charles University, 12800 Prague, Czech Republic
| | - Ondrej Machon
- Department of Developmental Biology, Institute of Experimental Medicine of the Czech Academy of Sciences, 14220 Prague, Czech Republic; (J.F.); (V.P.)
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14
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A Constrained Generalized Functional Linear Model for Multi-Loci Genetic Mapping. STATS 2021. [DOI: 10.3390/stats4030033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
In genome-wide association studies (GWAS), efficient incorporation of linkage disequilibria (LD) among densely typed genetic variants into association analysis is a critical yet challenging problem. Functional linear models (FLM), which impose a smoothing structure on the coefficients of correlated covariates, are advantageous in genetic mapping of multiple variants with high LD. Here we propose a novel constrained generalized FLM (cGFLM) framework to perform simultaneous association tests on a block of linked SNPs with various trait types, including continuous, binary and zero-inflated count phenotypes. The new cGFLM applies a set of inequality constraints on the FLM to ensure model identifiability under different genetic codings. The method is implemented via B-splines, and an augmented Lagrangian algorithm is employed for parameter estimation. For hypotheses testing, a test statistic that accounts for the model constraints was derived, following a mixture of chi-square distributions. Simulation results show that cGFLM is effective in identifying causal loci and gene clusters compared to several competing methods based on single markers and SKAT-C. We applied the proposed method to analyze a candidate gene-based COGEND study and a large-scale GWAS data on dental caries risk.
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15
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Deng Y, Meng M, Fang J, Jiang H, Sun N, Lv W, Lei Y, Wang C, Bo J, Liu C, Wang Y, Yang L, He S. Genome of the butterfly hillstream loach provides insights into adaptations to torrential mountain stream life. Mol Ecol Resour 2021; 21:1922-1935. [PMID: 33893720 DOI: 10.1111/1755-0998.13400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 03/25/2021] [Accepted: 04/13/2021] [Indexed: 11/27/2022]
Abstract
Butterfly hillstream loach (Beaufortia kweichowensis), a benthic fish in the torrential mountain streams, possesses a totally flat ventrum, flattened craniofacial and body skeletons, and enlarged paired fins covered by substantially small keratinous structures. However, little is known about the genetic basis of these specialized morphological adaptations. Here we present a 448.52-Mb genome assembly with contig N50 length of 5.53 Mb by integrating Illumina short-read sequencing, Nanopore long-read sequencing and HiC-based chromatin map. Demographic history reconstruction of the butterfly hillstream loach reveals that the population dynamics is correlated with the different stages of uplifting of the Tibetan Plateau. Comparative genomic analysis finds evidence of six keratin genes in butterfly hillstream loach evolving under positive selection. Within these genes, two keratin genes exhibit species-specific and divergent amino acid changes, suggesting a role in the formation of the unculi. Additionally, a series of positively selected genes, rapid evolving genes, specific variant genes and expanded gene families are found, including genes related to Hedgehog, Notch and BMP pathways, which may be involved in craniofacial development. These findings may have important implications for understanding the genetic basis of phenotypic adaptation to torrential mountain stream life.
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Affiliation(s)
- Yu Deng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Minghui Meng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jian Fang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Haifeng Jiang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ning Sun
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wenqi Lv
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yi Lei
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Cheng Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jing Bo
- University of Chinese Academy of Sciences, Beijing, China.,Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Chun Liu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Ying Wang
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, College of Life Sciences, Jianghan University, Wuhan, China
| | - Liandong Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Shunping He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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16
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Long F, Shi H, Li P, Guo S, Ma Y, Wei S, Li Y, Gao F, Gao S, Wang M, Duan R, Wang X, Yang K, Sun W, Li X, Li J, Liu Q. A SMOC2 variant inhibits BMP signaling by competitively binding to BMPR1B and causes growth plate defects. Bone 2021; 142:115686. [PMID: 33059102 DOI: 10.1016/j.bone.2020.115686] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/24/2020] [Accepted: 10/08/2020] [Indexed: 12/21/2022]
Abstract
Endochondral ossification is the major process of long bone formation, and chondrogenesis is the final step of this process. Several studies have indicated that bone morphogenetic proteins (BMPs) are required for chondrogenesis and regulate multiple growth plate features. Abnormal BMP pathways lead to growth plate defects, resulting in osteochondrodysplasia. The SPARC-related modular calcium binding 2 (SMOC2) gene encodes an extracellular protein that is considered to be an antagonist of BMP signaling. In this study, we generated a mouse model by knocking-in the SMOC2 mutation (c.1076 T > G), which showed short-limbed dwarfism, reduced, disorganized, and hypocellular proliferative zones and expanded hypertrophic zones in tibial growth plates. To determine the underlying pathophysiological mechanism of SMOC2 mutation, we used knock-in mice to investigate the interaction between SMOC2 and the BMP-SMAD1/5/9 signaling pathway in vivo and in vitro. Eventually, we found that mutant SMOC2 could not bind to COL9A1 and HSPG. Furthermore, mutant SMOC2 inhibited BMP signaling by competitively binding to BMPR1B, which lead to defects in growth plates and short-limbed dwarfism in knock-in mice.
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Affiliation(s)
- Feng Long
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Hongbiao Shi
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Pengyu Li
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Shaoqiang Guo
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Yuer Ma
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Shijun Wei
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Yan Li
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Fei Gao
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Shang Gao
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Meitian Wang
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Ruonan Duan
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; Department of Neurology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Xiaojing Wang
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Kun Yang
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Wenjie Sun
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Xi Li
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Jiangxia Li
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Qiji Liu
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China.
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17
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Morkmued S, Clauss F, Schuhbaur B, Fraulob V, Mathieu E, Hemmerlé J, Clevers H, Koo BK, Dollé P, Bloch-Zupan A, Niederreither K. Deficiency of the SMOC2 matricellular protein impairs bone healing and produces age-dependent bone loss. Sci Rep 2020; 10:14817. [PMID: 32908163 PMCID: PMC7481257 DOI: 10.1038/s41598-020-71749-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 08/06/2020] [Indexed: 12/16/2022] Open
Abstract
Secreted extracellular matrix components which regulate craniofacial development could be reactivated and play roles in adult wound healing. We report a patient with a loss-of-function of the secreted matricellular protein SMOC2 (SPARC related modular calcium binding 2) presenting severe oligodontia, microdontia, tooth root deficiencies, alveolar bone hypoplasia, and a range of skeletal malformations. Turning to a mouse model, Smoc2-GFP reporter expression indicates SMOC2 dynamically marks a range of dental and bone progenitors. While germline Smoc2 homozygous mutants are viable, tooth number anomalies, reduced tooth size, altered enamel prism patterning, and spontaneous age-induced periodontal bone and root loss are observed in this mouse model. Whole-genome RNA-sequencing analysis of embryonic day (E) 14.5 cap stage molars revealed reductions in early expressed enamel matrix components (Odontogenic ameloblast-associated protein) and dentin dysplasia targets (Dentin matrix acidic phosphoprotein 1). We tested if like other matricellular proteins SMOC2 was required for regenerative repair. We found that the Smoc2-GFP reporter was reactivated in adjacent periodontal tissues 4 days after tooth avulsion injury. Following maxillary tooth injury, Smoc2−/− mutants had increased osteoclast activity and bone resorption surrounding the extracted molar. Interestingly, a 10-day treatment with the cyclooxygenase 2 (COX2) inhibitor ibuprofen (30 mg/kg body weight) blocked tooth injury-induced bone loss in Smoc2−/− mutants, reducing matrix metalloprotease (Mmp)9. Collectively, our results indicate that endogenous SMOC2 blocks injury-induced jaw bone osteonecrosis and offsets age-induced periodontal decay.
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Affiliation(s)
- Supawich Morkmued
- Developmental Biology and Stem Cells Department, Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, BP 10142, 67404, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, INSERM U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France.,Faculty of Dentistry, Pediatrics Division, Preventive Department, Khon Kaen University, Khon Kaen, Thailand
| | - François Clauss
- Faculté de Chirurgie Dentaire, Université de Strasbourg, 8 rue Ste Elisabeth, 67000, Strasbourg, France.,Hôpitaux Universitaires de Strasbourg, Pôle de Médecine et Chirurgie Bucco-Dentaires, Centre de Référence des Maladies Rares Orales et Dentaires, CRMR O Rares, Filière TETECOU, ERN CRANIO, 1 place de l'Hôpital, 67000, Strasbourg, France.,Regenerative NanoMedicine, INSERM UMR1260, FMTS, Hôpitaux Universitaires de Strasbourg, 11 rue Humann, 67000, Strasbourg, France
| | - Brigitte Schuhbaur
- Developmental Biology and Stem Cells Department, Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, BP 10142, 67404, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, INSERM U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Valérie Fraulob
- Developmental Biology and Stem Cells Department, Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, BP 10142, 67404, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, INSERM U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Eric Mathieu
- Biomaterials and Bioengineering, Université de Strasbourg, INSERM UMR1121, 11 rue Humann, 67000, Strasbourg, France
| | - Joseph Hemmerlé
- Biomaterials and Bioengineering, Université de Strasbourg, INSERM UMR1121, 11 rue Humann, 67000, Strasbourg, France
| | - Hans Clevers
- Hubrecht Institute, University Medical Center Utrecht, and University Utrecht, Utrecht, The Netherlands
| | - Bon-Kyoung Koo
- Hubrecht Institute, University Medical Center Utrecht, and University Utrecht, Utrecht, The Netherlands
| | - Pascal Dollé
- Developmental Biology and Stem Cells Department, Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, BP 10142, 67404, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, INSERM U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France.,Faculté de Médecine, Université de Strasbourg, FMTS, 4 Rue Kirschleger, 67000, Strasbourg, France
| | - Agnès Bloch-Zupan
- Developmental Biology and Stem Cells Department, Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, BP 10142, 67404, Illkirch, France. .,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France. .,Institut National de la Santé et de la Recherche Médicale, INSERM U1258, Illkirch, France. .,Université de Strasbourg, Illkirch, France. .,Faculté de Chirurgie Dentaire, Université de Strasbourg, 8 rue Ste Elisabeth, 67000, Strasbourg, France. .,Hôpitaux Universitaires de Strasbourg, Pôle de Médecine et Chirurgie Bucco-Dentaires, Centre de Référence des Maladies Rares Orales et Dentaires, CRMR O Rares, Filière TETECOU, ERN CRANIO, 1 place de l'Hôpital, 67000, Strasbourg, France. .,Eastman Dental Institute, University College London, London, UK.
| | - Karen Niederreither
- Developmental Biology and Stem Cells Department, Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, BP 10142, 67404, Illkirch, France. .,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France. .,Institut National de la Santé et de la Recherche Médicale, INSERM U1258, Illkirch, France. .,Université de Strasbourg, Illkirch, France. .,Faculté de Chirurgie Dentaire, Université de Strasbourg, 8 rue Ste Elisabeth, 67000, Strasbourg, France.
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18
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Secreted modular calcium-binding proteins in pathophysiological processes and embryonic development. Chin Med J (Engl) 2020; 132:2476-2484. [PMID: 31613820 PMCID: PMC6831058 DOI: 10.1097/cm9.0000000000000472] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Objective: Secreted modular calcium-binding proteins (SMOCs) are extracellular glycoproteins of the secreted protein, acidic, and rich in cysteine-related modular calcium-binding protein family and include two isoforms, SMOC1 and SMOC2, in humans. Functionally, SMOCs bind to calcium for various cell functions. In this review, we provided a summary of the most recent advancements in and findings of SMOC1 and SMOC2 in development, homeostasis, and disease states. Data sources: All publications in the PubMed database were searched and retrieved (up to July 24, 2019) using various combinations of keywords searching, including SMOC1, SMOC2, and diseases. Study selection: All original studies and review articles of SMOCs in human diseases and embryo development written in English were retrieved and included. Results: SMOC1 and SMOC2 regulate embryonic development, cell homeostasis, and disease pathophysiology. They play an important role in the regulation of cell cycle progression, cell attachment to the extracellular matrix, tissue fibrosis, calcification, angiogenesis, birth defects, and cancer development. Conclusions: SMOC1 and SMOC2 are critical regulators of many cell biological processes and potential therapeutic targets for the control of human cancers and birth defects.
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19
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Messina A, Pulli K, Santini S, Acierno J, Känsäkoski J, Cassatella D, Xu C, Casoni F, Malone SA, Ternier G, Conte D, Sidis Y, Tommiska J, Vaaralahti K, Dwyer A, Gothilf Y, Merlo GR, Santoni F, Niederländer NJ, Giacobini P, Raivio T, Pitteloud N. Neuron-Derived Neurotrophic Factor Is Mutated in Congenital Hypogonadotropic Hypogonadism. Am J Hum Genet 2020; 106:58-70. [PMID: 31883645 DOI: 10.1016/j.ajhg.2019.12.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 11/22/2019] [Indexed: 12/20/2022] Open
Abstract
Congenital hypogonadotropic hypogonadism (CHH) is a rare genetic disorder characterized by infertility and the absence of puberty. Defects in GnRH neuron migration or altered GnRH secretion and/or action lead to a severe gonadotropin-releasing hormone (GnRH) deficiency. Given the close developmental association of GnRH neurons with the olfactory primary axons, CHH is often associated with anosmia or hyposmia, in which case it is defined as Kallmann syndrome (KS). The genetics of CHH are heterogeneous, and >40 genes are involved either alone or in combination. Several CHH-related genes controlling GnRH ontogeny encode proteins containing fibronectin-3 (FN3) domains, which are important for brain and neural development. Therefore, we hypothesized that defects in other FN3-superfamily genes would underlie CHH. Next-generation sequencing was performed for 240 CHH unrelated probands and filtered for rare, protein-truncating variants (PTVs) in FN3-superfamily genes. Compared to gnomAD controls the CHH cohort was statistically enriched for PTVs in neuron-derived neurotrophic factor (NDNF) (p = 1.40 × 10-6). Three heterozygous PTVs (p.Lys62∗, p.Tyr128Thrfs∗55, and p.Trp469∗, all absent from the gnomAD database) and an additional heterozygous missense mutation (p.Thr201Ser) were found in four KS probands. Notably, NDNF is expressed along the GnRH neuron migratory route in both mouse embryos and human fetuses and enhances GnRH neuron migration. Further, knock down of the zebrafish ortholog of NDNF resulted in altered GnRH migration. Finally, mice lacking Ndnf showed delayed GnRH neuron migration and altered olfactory axonal projections to the olfactory bulb; both results are consistent with a role of NDNF in GnRH neuron development. Altogether, our results highlight NDNF as a gene involved in the GnRH neuron migration implicated in KS.
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Affiliation(s)
- Andrea Messina
- Service of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - Kristiina Pulli
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Sara Santini
- Service of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - James Acierno
- Service of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, 1011 Lausanne, Switzerland; Università Vita-Salute San Raffaele, Via Olgettina 58, 20132, Milan, Italy
| | - Johanna Känsäkoski
- Department of Physiology, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Daniele Cassatella
- Service of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, 1011 Lausanne, Switzerland; Università Vita-Salute San Raffaele, Via Olgettina 58, 20132, Milan, Italy
| | - Cheng Xu
- Service of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - Filippo Casoni
- Inserm, Jean-Pierre Aubert Research Center, Development and Plasticity of the Neuroendocrine Brain, Unité 1172 Lille, 59045 Lille, France; Division of Neuroscience, San Raffaele Scientific Institute, Milan 20132, Italy, Milan 20132, Italy; Università Vita-Salute San Raffaele, Via Olgettina 58, 20132, Milan, Italy
| | - Samuel A Malone
- Inserm, Jean-Pierre Aubert Research Center, Development and Plasticity of the Neuroendocrine Brain, Unité 1172 Lille, 59045 Lille, France
| | - Gaetan Ternier
- Inserm, Jean-Pierre Aubert Research Center, Development and Plasticity of the Neuroendocrine Brain, Unité 1172 Lille, 59045 Lille, France
| | - Daniele Conte
- Department of Molecular Biotechnology and Health Science, University of Torino, 10126 Torino, Italy
| | - Yisrael Sidis
- Service of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - Johanna Tommiska
- Department of Physiology, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Kirsi Vaaralahti
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Andrew Dwyer
- Service of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - Yoav Gothilf
- Department of Neurobiology, George S. Wise Faculty of Life Sciences and Sagol School of Neurosciences, University of Tel Aviv, Tel Aviv 69978, Israel
| | - Giorgio R Merlo
- Department of Molecular Biotechnology and Health Science, University of Torino, 10126 Torino, Italy
| | - Federico Santoni
- Service of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - Nicolas J Niederländer
- Service of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - Paolo Giacobini
- Inserm, Jean-Pierre Aubert Research Center, Development and Plasticity of the Neuroendocrine Brain, Unité 1172 Lille, 59045 Lille, France
| | - Taneli Raivio
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland; Pediatric Research Center, New Children's Hospital, Helsinki University Hospital, 00290 Helsinki, Finland
| | - Nelly Pitteloud
- Service of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, 1011 Lausanne, Switzerland; Faculty of Biology and Medicine, University of Lausanne, Lausanne 1005, Switzerland.
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20
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Tapia-Carrillo D, Tovar H, Velazquez-Caldelas TE, Hernandez-Lemus E. Master Regulators of Signaling Pathways: An Application to the Analysis of Gene Regulation in Breast Cancer. Front Genet 2019; 10:1180. [PMID: 31850059 PMCID: PMC6902642 DOI: 10.3389/fgene.2019.01180] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 10/24/2019] [Indexed: 12/13/2022] Open
Abstract
Analysis of gene regulatory networks allows the identification of master transcriptional factors that control specific groups of genes. In this work, we inferred a gene regulatory network from a large dataset of breast cancer samples to identify the master transcriptional factors that control the genes within signal transduction pathways. The focus in a particular subset of relevant genes constitutes an extension of the original Master Regulator Inference Algorithm (MARINa) analysis. This modified version of MARINa utilizes a restricted molecular signature containing genes from the 25 human pathways in KEGG's signal transduction category. Our breast cancer RNAseq expression dataset consists of 881 samples comprising tumors and normal mammary gland tissue. The top 10 master transcriptional factors found to regulate signal transduction pathways in breast cancer we identified are: TSHZ2, HOXA2, MEIS2, HOXA3, HAND2, HOXA5, TBX18, PEG3, GLI2, and CLOCK. The functional enrichment of the regulons of these master transcriptional factors showed an important proportion of processes related to morphogenesis. Our results suggest that, as part of the aberrant regulation of signaling pathways in breast cancer, pathways similar to the regulation of cell differentiation, cardiovascular system development, and vasculature development may be dysregulated and co-opted in favor of tumor development through the action of these transcription factors.
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Affiliation(s)
- Diana Tapia-Carrillo
- Computational Genomics Department, National Institute of Genomic Medicine (INMEGEN), Mexico City, Mexico.,Graduate Program in Biological Sciences, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | - Hugo Tovar
- Computational Genomics Department, National Institute of Genomic Medicine (INMEGEN), Mexico City, Mexico
| | | | - Enrique Hernandez-Lemus
- Computational Genomics Department, National Institute of Genomic Medicine (INMEGEN), Mexico City, Mexico.,Center for Complexity Sciences, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
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21
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Fillatre J, Fauny JD, Fels JA, Li C, Goll M, Thisse C, Thisse B. TEADs, Yap, Taz, Vgll4s transcription factors control the establishment of Left-Right asymmetry in zebrafish. eLife 2019; 8:45241. [PMID: 31513014 PMCID: PMC6759317 DOI: 10.7554/elife.45241] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 09/11/2019] [Indexed: 12/15/2022] Open
Abstract
In many vertebrates, establishment of Left-Right (LR) asymmetry results from the activity of a ciliated organ functioning as the LR Organizer (LRO). While regulation of the formation of this structure by major signaling pathways has been described, the transcriptional control of LRO formation is poorly understood. Using the zebrafish model, we show that the transcription factors and cofactors mediating or regulating the transcriptional outcome of the Hippo signaling pathway play a pivotal role in controlling the expression of genes essential to the formation of the LRO including ligands and receptors of signaling pathways involved in this process and most genes required for motile ciliogenesis. Moreover, the transcription cofactor, Vgll4l regulates epigenetic programming in LRO progenitors by controlling the expression of writers and readers of DNA methylation marks. Altogether, our study uncovers a novel and essential role for the transcriptional effectors and regulators of the Hippo pathway in establishing LR asymmetry.
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Affiliation(s)
- Jonathan Fillatre
- Department of Cell Biology, University of Virginia, Charlottesville, United States
| | - Jean-Daniel Fauny
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/Université de Strasbourg, Illkirch-Graffenstaden, France.,Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | | | - Cheng Li
- Department of Genetics, University of Georgia, Athens, United States
| | - Mary Goll
- Department of Genetics, University of Georgia, Athens, United States
| | - Christine Thisse
- Department of Cell Biology, University of Virginia, Charlottesville, United States.,Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/Université de Strasbourg, Illkirch-Graffenstaden, France
| | - Bernard Thisse
- Department of Cell Biology, University of Virginia, Charlottesville, United States.,Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/Université de Strasbourg, Illkirch-Graffenstaden, France
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22
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Negri A, Ferrari M, Nodari R, Coppa E, Mastrantonio V, Zanzani S, Porretta D, Bandi C, Urbanelli S, Epis S. Gene silencing through RNAi and antisense Vivo-Morpholino increases the efficacy of pyrethroids on larvae of Anopheles stephensi. Malar J 2019; 18:294. [PMID: 31462239 PMCID: PMC6712854 DOI: 10.1186/s12936-019-2925-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/17/2019] [Indexed: 11/25/2022] Open
Abstract
Background Insecticides are still at the core of insect pest and vector control programmes. Several lines of evidence indicate that ABC transporters are involved in detoxification processes against insecticides, including permethrin and other pyrethroids. In particular, the ABCG4 gene, a member of the G subfamily, has consistently been shown to be up-regulated in response to insecticide treatments in the mosquito malaria vector Anopheles stephensi (both adults and larvae). Methods To verify the actual involvement of this transmembrane protein in the detoxification process of permethrin, bioassays on larvae of An. stephensi, combining the insecticide with a siRNA, specifically designed for the inhibition of ABCG4 gene expression were performed. Administration to larvae of the same siRNA, labeled with a fluorescent molecule, was effected to investigate the systemic distribution of the inhibitory RNA into the larval bodies. Based on siRNA results, similar experiments using antisense Vivo-Morpholinos (Vivo-MOs) were effected. These molecules, compared to siRNA, are expected to guarantee a higher stability in environmental conditions and in the insect gut, and present thus a higher potential for future in-field applications. Results Bioassays using two different concentrations of siRNA, associated with permethrin, led to an increase of larval mortality, compared with results with permethrin alone. These outcomes confirm that ABCG4 transporter plays a role in the detoxification process against the selected insecticide. Moreover, after fluorescent labelling, it was shown the systemic dissemination of siRNA in different body districts of An. stephensi larvae, which suggest a potential systemic effect of the molecule. At the same time, results of Vivo-MO experiments were congruent with those obtained using siRNA, thus confirming the potential of ABCG4 inhibition as a strategy to increase permethrin susceptibility in mosquitoes. For the first time, Vivo-MOs were administered in water to larvae, with evidence for a biological effect. Conclusions Targeting ABCG4 gene for silencing through both techniques resulted in an increased pyrethroid efficacy. These results open the way toward the possibility to exploit ABCG4 inhibition in the context of integrated programmes for the control An. stephensi mosquitoes and malaria transmission.
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Affiliation(s)
- Agata Negri
- Department of Environmental Biology, Sapienza University of Rome, Via dei Sardi 70, 00185, Rome, Italy.,Department of Biosciences and Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", University of Milan, Via Celoria 26, 20133, Milan, Italy.,Centro Interuniversitario di Ricerca sulla Malaria/Italian Malaria Network, Via del Giochetto, 06126, Perugia, Italy
| | - Marco Ferrari
- Department of Biosciences and Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", University of Milan, Via Celoria 26, 20133, Milan, Italy.,Texas Biomedical Research Institute, San Antonio, 7620 NW Loop 410, San Antonio, TX, 78227-5301, USA
| | - Riccardo Nodari
- Department of Biosciences and Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", University of Milan, Via Celoria 26, 20133, Milan, Italy.,Centro Interuniversitario di Ricerca sulla Malaria/Italian Malaria Network, Via del Giochetto, 06126, Perugia, Italy
| | - Edoardo Coppa
- Department of Biosciences and Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", University of Milan, Via Celoria 26, 20133, Milan, Italy
| | - Valentina Mastrantonio
- Department of Environmental Biology, Sapienza University of Rome, Via dei Sardi 70, 00185, Rome, Italy
| | - Sergio Zanzani
- Department of Veterinary Medicine-DIMEVET, Università degli Studi di Milano, Via Celoria, 10, 20133, Milan, Italy
| | - Daniele Porretta
- Department of Environmental Biology, Sapienza University of Rome, Via dei Sardi 70, 00185, Rome, Italy
| | - Claudio Bandi
- Department of Biosciences and Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", University of Milan, Via Celoria 26, 20133, Milan, Italy.,Centro Interuniversitario di Ricerca sulla Malaria/Italian Malaria Network, Via del Giochetto, 06126, Perugia, Italy
| | - Sandra Urbanelli
- Department of Environmental Biology, Sapienza University of Rome, Via dei Sardi 70, 00185, Rome, Italy
| | - Sara Epis
- Department of Biosciences and Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", University of Milan, Via Celoria 26, 20133, Milan, Italy. .,Centro Interuniversitario di Ricerca sulla Malaria/Italian Malaria Network, Via del Giochetto, 06126, Perugia, Italy.
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23
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Decoding and targeting the molecular basis of MACC1-driven metastatic spread: Lessons from big data mining and clinical-experimental approaches. Semin Cancer Biol 2019; 60:365-379. [PMID: 31430556 DOI: 10.1016/j.semcancer.2019.08.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/09/2019] [Accepted: 08/09/2019] [Indexed: 12/17/2022]
Abstract
Metastasis remains the key issue impacting cancer patient survival and failure or success of cancer therapies. Metastatic spread is a complex process including dissemination of single cells or collective cell migration, penetration of the blood or lymphatic vessels and seeding at a distant organ site. Hundreds of genes involved in metastasis have been identified in studies across numerous cancer types. Here, we analyzed how the metastasis-associated gene MACC1 cooperates with other genes in metastatic spread and how these coactions could be exploited by combination therapies: We performed (i) a MACC1 correlation analysis across 33 cancer types in the mRNA expression data of TCGA and (ii) a comprehensive literature search on reported MACC1 combinations and regulation mechanisms. The key genes MET, HGF and MMP7 reported together with MACC1 showed significant positive correlations with MACC1 in more than half of the cancer types included in the big data analysis. However, ten other genes also reported together with MACC1 in the literature showed significant positive correlations with MACC1 in only a minority of 5 to 15 cancer types. To uncover transcriptional regulation mechanisms that are activated simultaneously with MACC1, we isolated pan-cancer consensus lists of 1306 positively and 590 negatively MACC1-correlating genes from the TCGA data and analyzed each of these lists for sharing transcription factor binding motifs in the promotor region. In these lists, binding sites for the transcription factors TELF1, ETS2, ETV4, TEAD1, FOXO4, NFE2L1, ELK1, SP1 and NFE2L2 were significantly enriched, but none of them except SP1 was reported in combination with MACC1 in the literature. Thus, while some of the results of the big data analysis were in line with the reported experimental results, hypotheses on new genes involved in MACC1-driven metastasis formation could be generated and warrant experimental validation. Furthermore, the results of the big data analysis can help to prioritize cancer types for experimental studies and testing of combination therapies.
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24
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Schulte D, Geerts D. MEIS transcription factors in development and disease. Development 2019; 146:146/16/dev174706. [PMID: 31416930 DOI: 10.1242/dev.174706] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 06/28/2019] [Indexed: 12/12/2022]
Abstract
MEIS transcription factors are key regulators of embryonic development and cancer. Research on MEIS genes in the embryo and in stem cell systems has revealed novel and surprising mechanisms by which these proteins control gene expression. This Primer summarizes recent findings about MEIS protein activity and regulation in development, and discusses new insights into the role of MEIS genes in disease, focusing on the pathogenesis of solid cancers.
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Affiliation(s)
- Dorothea Schulte
- Institute of Neurology (Edinger Institute), University Hospital Frankfurt, Goethe University, 60528 Frankfurt, Germany
| | - Dirk Geerts
- Department of Medical Biology L2-109, Amsterdam University Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
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25
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Radhakrishnan H, Walther W, Zincke F, Kobelt D, Imbastari F, Erdem M, Kortüm B, Dahlmann M, Stein U. MACC1-the first decade of a key metastasis molecule from gene discovery to clinical translation. Cancer Metastasis Rev 2019; 37:805-820. [PMID: 30607625 DOI: 10.1007/s10555-018-9771-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Deciphering the paths to metastasis and identifying key molecules driving this process is one important issue for understanding and treatment of cancer. Such a key driver molecule is Metastasis Associated in Colon Cancer 1 (MACC1). A decade long research on this evolutionarily conserved molecule with features of a transcription factor as well as an adapter protein for versatile protein-protein interactions has shown that it has manifold properties driving tumors to their metastatic stage. MACC1 transcriptionally regulates genes involved in epithelial-mesenchymal transition (EMT), including those which are able to directly induce metastasis like c-MET, impacts tumor cell migration and invasion, and induces metastasis in solid cancers. MACC1 has proven as a valuable biomarker for prognosis of metastasis formation linked to patient survival and gives promise to also act as a predictive marker for individualized therapies in a broad variety of cancers. This review discusses the many features of MACC1 in the context of the hallmarks of cancer and the potential of this molecule as biomarker and novel therapeutic target for restriction and prevention of metastasis.
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Affiliation(s)
- Harikrishnan Radhakrishnan
- Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Wolfgang Walther
- Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125, Berlin, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center, Heidelberg, Germany
| | - Fabian Zincke
- Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125, Berlin, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center, Heidelberg, Germany
| | - Dennis Kobelt
- Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125, Berlin, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center, Heidelberg, Germany
| | - Francesca Imbastari
- Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Müge Erdem
- Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Benedikt Kortüm
- Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Mathias Dahlmann
- Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125, Berlin, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center, Heidelberg, Germany
| | - Ulrike Stein
- Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125, Berlin, Germany. .,German Cancer Consortium (DKTK), German Cancer Research Center, Heidelberg, Germany.
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26
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Heterozygous loss-of-function variants of MEIS2 cause a triad of palatal defects, congenital heart defects, and intellectual disability. Eur J Hum Genet 2018; 27:278-290. [PMID: 30291340 DOI: 10.1038/s41431-018-0281-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 07/03/2018] [Accepted: 07/15/2018] [Indexed: 12/14/2022] Open
Abstract
Deletions on chromosome 15q14 are a known chromosomal cause of cleft palate, typically co-occurring with intellectual disability, facial dysmorphism, and congenital heart defects. The identification of patients with loss-of-function variants in MEIS2, a gene within this deletion, suggests that these features are attributed to haploinsufficiency of MEIS2. To further delineate the phenotypic spectrum of the MEIS2-related syndrome, we collected 23 previously unreported patients with either a de novo sequence variant in MEIS2 (9 patients), or a 15q14 microdeletion affecting MEIS2 (14 patients). All but one de novo MEIS2 variant were identified by whole-exome sequencing. One variant was found by targeted sequencing of MEIS2 in a girl with a clinical suspicion of this syndrome. In addition to the triad of palatal defects, heart defects, and developmental delay, heterozygous loss of MEIS2 results in recurrent facial features, including thin and arched eyebrows, short alae nasi, and thin vermillion. Genotype-phenotype comparison between patients with 15q14 deletions and patients with sequence variants or intragenic deletions within MEIS2, showed a higher prevalence of moderate-to-severe intellectual disability in the former group, advocating for an independent locus for psychomotor development neighboring MEIS2.
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Peeters T, Monteagudo S, Tylzanowski P, Luyten FP, Lories R, Cailotto F. SMOC2 inhibits calcification of osteoprogenitor and endothelial cells. PLoS One 2018; 13:e0198104. [PMID: 29897942 PMCID: PMC5999237 DOI: 10.1371/journal.pone.0198104] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 05/14/2018] [Indexed: 11/18/2022] Open
Abstract
Tissue calcification is an important physiological process required for the normal structure and function of bone. However, ectopic or excessive calcification contributes to diseases such as chondrocalcinosis, to calcium deposits in the skin or to vascular calcification. SMOC2 is a member of the BM-40/osteonectin family of calcium-binding secreted matricellular proteins. Using osteoprogenitor MC3T3-E1 cells stably overexpressing SMOC2, we show that SMOC2 inhibits osteogenic differentiation and extracellular matrix mineralization. Stable Smoc2 knockdown in these cells had no effect on mineralization suggesting that endogenous SMOC2 is not essential for the mineralization process. Mineralization in MC3T3-E1 cells overexpressing mutant SMOC2 lacking the extracellular calcium-binding domain was significantly increased compared to cells overexpressing full length SMOC2. When SMOC2 overexpressing cells were cultured in the presence of extracellular calcium supplementation, SMOC2’s inhibitory effect on calcification was rescued. Our observations were translationally validated in primary human periosteal-derived cells. Furthermore, SMOC2 was able to impair mineralization in transdifferentiated human umbilical vein endothelial cells. Taken together, our data indicate that SMOC2 can act as an inhibitor of mineralization. We propose a possible role for SMOC2 to prevent calcification disorders.
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Affiliation(s)
- Tine Peeters
- Laboratory of Tissue Homeostasis and Disease, Skeletal Biology and Engineering Research Center, Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Silvia Monteagudo
- Laboratory of Tissue Homeostasis and Disease, Skeletal Biology and Engineering Research Center, Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Przemko Tylzanowski
- Laboratory for Developmental and Stem Cell Biology, Skeletal Biology and Engineering Research Center, Department of Development and Regeneration, KU Leuven, Leuven, Belgium
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Lublin, Poland
| | - Frank P. Luyten
- Laboratory for Developmental and Stem Cell Biology, Skeletal Biology and Engineering Research Center, Department of Development and Regeneration, KU Leuven, Leuven, Belgium
- Division of Rheumatology, University Hospitals Leuven, Leuven, Belgium
| | - Rik Lories
- Laboratory of Tissue Homeostasis and Disease, Skeletal Biology and Engineering Research Center, Department of Development and Regeneration, KU Leuven, Leuven, Belgium
- Division of Rheumatology, University Hospitals Leuven, Leuven, Belgium
- * E-mail:
| | - Frédéric Cailotto
- Laboratory of Tissue Homeostasis and Disease, Skeletal Biology and Engineering Research Center, Department of Development and Regeneration, KU Leuven, Leuven, Belgium
- UMR 7365 CNRS‐Université de Lorraine, Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), Biopôle de l’Université de Lorraine, Campus Biologie-Santé, Vandoeuvre Les Nancy, France
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28
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Abstract
The extracellular matrix (ECM) has central roles in tissue integrity and remodeling throughout the life span of animals. While collagens are the most abundant structural components of ECM in most tissues, tissue-specific molecular complexity is contributed by ECM glycoproteins. The matricellular glycoproteins are categorized primarily according to functional criteria and represented predominantly by the thrombospondin, tenascin, SPARC/osteonectin, and CCN families. These proteins do not self-assemble into ECM fibrils; nevertheless, they shape ECM properties through interactions with structural ECM proteins, growth factors, and cells. Matricellular proteins also promote cell migration or morphological changes through adhesion-modulating or counter-adhesive actions on cell-ECM adhesions, intracellular signaling, and the actin cytoskeleton. Typically, matricellular proteins are most highly expressed during embryonic development. In adult tissues, expression is more limited unless activated by cues for dynamic tissue remodeling and cell motility, such as occur during inflammatory response and wound repair. Many insights in the complex roles of matricellular proteins have been obtained from studies of gene knockout mice. However, with the exception of chordate-specific tenascins, these are highly conserved proteins that are encoded in many animal phyla. This review will consider the increasing body of research on matricellular proteins in nonmammalian animal models. These models provide better access to the very earliest stages of embryonic development and opportunities to study biological processes such as limb and organ regeneration. In aggregate, this research is expanding concepts of the functions and mechanisms of action of matricellular proteins.
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Affiliation(s)
- Josephine C Adams
- School of Biochemistry, University of Bristol, Bristol, United Kingdom.
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29
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Xue C, Wang HH, Zhu J, Zhou J. The expression patterns of vestigial like family member 4 genes in zebrafish embryogenesis. Gene Expr Patterns 2018; 28:34-41. [PMID: 29454044 DOI: 10.1016/j.gep.2018.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 01/11/2018] [Accepted: 02/05/2018] [Indexed: 11/30/2022]
Abstract
Transcriptional cofactor Vestigial-like 4 (VGLL4) was considered to take part in the early stage of development. Different from human, three paralogs of vgll4 were found in zebrafish, which were vgll4a, vgll4b and vgll4l. However, the expression patterns of the three paralogs during zebrafish development remains unknown. In this study, we used in situ hybridization to elucidate the temporal and spatial expression of zebrafish vgll4 paralogs during normal embryonic and larval development. Similar expression was shown in certain areas at similar stages for the three paralogs. Expression of vgll4a, vgll4b and vgll4l were all found in pectoral fins and otic vesicles during the early developmental stages. On the other hand, a few differences of the three paralogs expression were found in eyes, pharynx, pharyngeal arches and brain tissues. The expression of vgll4a was weak and ubiquitous, while vgll4b was obviously expressed in brain tissues and vgll4l was clearly restricted to each pair of pharyngeal pouches. What's more, vgll4b and vgll4l had unique expression at mature lateral line neuromasts and forerunner cells respectively. Despite the conservativeness of functional domains, the three paralogs of zebrafish vgll4 shared several similarities and displayed some distinctions in the expression patterns, indicating that they may still have different and exclusive functions, which need to be further explored.
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Affiliation(s)
- Chang Xue
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Hai Hong Wang
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Jun Zhu
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Jun Zhou
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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30
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Identification of stiffness-induced signalling mechanisms in cells from patent and fused sutures associated with craniosynostosis. Sci Rep 2017; 7:11494. [PMID: 28904366 PMCID: PMC5597583 DOI: 10.1038/s41598-017-11801-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 08/30/2017] [Indexed: 11/08/2022] Open
Abstract
Craniosynostosis is a bone developmental disease where premature ossification of the cranial sutures occurs leading to fused sutures. While biomechanical forces have been implicated in craniosynostosis, evidence of the effect of microenvironmental stiffness changes in the osteogenic commitment of cells from the sutures is lacking. Our aim was to identify the differential genetic expression and osteogenic capability between cells from patent and fused sutures of children with craniosynostosis and whether these differences are driven by changes in the stiffness of the microenvironment. Cells from both sutures demonstrated enhanced mineralisation with increasing substrate stiffness showing that stiffness is a stimulus capable of triggering the accelerated osteogenic commitment of the cells from patent to fused stages. The differences in the mechanoresponse of these cells were further investigated with a PCR array showing stiffness-dependent upregulation of genes mediating growth and bone development (TSHZ2, IGF1), involved in the breakdown of extracellular matrix (MMP9), mediating the activation of inflammation (IL1β) and controlling osteogenic differentiation (WIF1, BMP6, NOX1) in cells from fused sutures. In summary, this study indicates that stiffer substrates lead to greater osteogenic commitment and accelerated bone formation, suggesting that stiffening of the extracellular environment may trigger the premature ossification of the sutures.
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31
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Ludwig KU, Böhmer AC, Bowes J, Nikolic M, Ishorst N, Wyatt N, Hammond NL, Gölz L, Thieme F, Barth S, Schuenke H, Klamt J, Spielmann M, Aldhorae K, Rojas-Martinez A, Nöthen MM, Rada-Iglesias A, Dixon MJ, Knapp M, Mangold E. Imputation of orofacial clefting data identifies novel risk loci and sheds light on the genetic background of cleft lip ± cleft palate and cleft palate only. Hum Mol Genet 2017; 26:829-842. [PMID: 28087736 PMCID: PMC5409059 DOI: 10.1093/hmg/ddx012] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 01/09/2017] [Indexed: 12/22/2022] Open
Abstract
Nonsyndromic cleft lip with or without cleft palate (nsCL/P) is among the most common human birth defects with multifactorial etiology. Here, we present results from a genome-wide imputation study of nsCL/P in which, after adding replication cohort data, four novel risk loci for nsCL/P are identified (at chromosomal regions 2p21, 14q22, 15q24 and 19p13). On a systematic level, we show that the association signals within this high-density dataset are enriched in functionally-relevant genomic regions that are active in both human neural crest cells (hNCC) and mouse embryonic craniofacial tissue. This enrichment is also detectable in hNCC regions primed for later activity. Using GCTA analyses, we suggest that 30% of the estimated variance in risk for nsCL/P in the European population can be attributed to common variants, with 25.5% contributed to by the 24 risk loci known to date. For each of these, we identify credible SNPs using a Bayesian refinement approach, with two loci harbouring only one probable causal variant. Finally, we demonstrate that there is no polygenic component of nsCL/P detectable that is shared with nonsyndromic cleft palate only (nsCPO). Our data suggest that, while common variants are strongly contributing to risk for nsCL/P, they do not seem to be involved in nsCPO which might be more often caused by rare deleterious variants. Our study generates novel insights into both nsCL/P and nsCPO etiology and provides a systematic framework for research into craniofacial development and malformation.
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Affiliation(s)
- Kerstin U Ludwig
- Institute of Human Genetics University of Bonn, Bonn 53127, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn 53127, Germany
| | - Anne C Böhmer
- Institute of Human Genetics University of Bonn, Bonn 53127, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn 53127, Germany
| | - John Bowes
- Arthritis Research UK Centre for Genetics and Genomics, The University of Manchester, Manchester M13 9PT, UK
| | - Miloš Nikolic
- Center for Molecular Medicine Cologne.,Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| | - Nina Ishorst
- Institute of Human Genetics University of Bonn, Bonn 53127, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn 53127, Germany
| | - Niki Wyatt
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Nigel L Hammond
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Lina Gölz
- Department of Orthodontics, University of Bonn, Bonn 53111, Germany
| | - Frederic Thieme
- Institute of Human Genetics University of Bonn, Bonn 53127, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn 53127, Germany
| | - Sandra Barth
- Institute of Human Genetics University of Bonn, Bonn 53127, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn 53127, Germany
| | - Hannah Schuenke
- Institute of Human Genetics University of Bonn, Bonn 53127, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn 53127, Germany
| | - Johanna Klamt
- Institute of Human Genetics University of Bonn, Bonn 53127, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn 53127, Germany
| | - Malte Spielmann
- Max Planck Institute for Molecular Genetics, RG Development and Disease, Berlin 14195, Germany.,Institute for Medical and Human Genetics.,Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, Berlin 13353, Germany
| | - Khalid Aldhorae
- Orthodontic Department, College of Dentistry, Thamar University, Thamar, Yemen
| | - Augusto Rojas-Martinez
- Tecnologico de Monterrey, School of Medicine, and Universidad Autonoma de Nuevo Leon, Centro de Investigación y Desarrollo en Ciencias de la Salud, Monterrey 64460, Mexico
| | - Markus M Nöthen
- Institute of Human Genetics University of Bonn, Bonn 53127, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn 53127, Germany
| | - Alvaro Rada-Iglesias
- Center for Molecular Medicine Cologne.,Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| | - Michael J Dixon
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Michael Knapp
- Institute of Medical Biometry, Informatics and Epidemiology, University of Bonn, Bonn 53127, Germany
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32
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Marchant TW, Johnson EJ, McTeir L, Johnson CI, Gow A, Liuti T, Kuehn D, Svenson K, Bermingham ML, Drögemüller M, Nussbaumer M, Davey MG, Argyle DJ, Powell RM, Guilherme S, Lang J, Ter Haar G, Leeb T, Schwarz T, Mellanby RJ, Clements DN, Schoenebeck JJ. Canine Brachycephaly Is Associated with a Retrotransposon-Mediated Missplicing of SMOC2. Curr Biol 2017; 27:1573-1584.e6. [PMID: 28552356 PMCID: PMC5462623 DOI: 10.1016/j.cub.2017.04.057] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 03/14/2017] [Accepted: 04/27/2017] [Indexed: 12/30/2022]
Abstract
In morphological terms, “form” is used to describe an object’s shape and size. In dogs, facial form is stunningly diverse. Facial retrusion, the proximodistal shortening of the snout and widening of the hard palate is common to brachycephalic dogs and is a welfare concern, as the incidence of respiratory distress and ocular trauma observed in this class of dogs is highly correlated with their skull form. Progress to identify the molecular underpinnings of facial retrusion is limited to association of a missense mutation in BMP3 among small brachycephalic dogs. Here, we used morphometrics of skull isosurfaces derived from 374 pedigree and mixed-breed dogs to dissect the genetics of skull form. Through deconvolution of facial forms, we identified quantitative trait loci that are responsible for canine facial shapes and sizes. Our novel insights include recognition that the FGF4 retrogene insertion, previously associated with appendicular chondrodysplasia, also reduces neurocranium size. Focusing on facial shape, we resolved a quantitative trait locus on canine chromosome 1 to a 188-kb critical interval that encompasses SMOC2. An intronic, transposable element within SMOC2 promotes the utilization of cryptic splice sites, causing its incorporation into transcripts, and drastically reduces SMOC2 gene expression in brachycephalic dogs. SMOC2 disruption affects the facial skeleton in a dose-dependent manner. The size effects of the associated SMOC2 haplotype are profound, accounting for 36% of facial length variation in the dogs we tested. Our data bring new focus to SMOC2 by highlighting its clinical implications in both human and veterinary medicine. A population-based genetics study of dogs that required diagnostic imaging Resolution of a QTL associated with face length reduction (brachycephaly) Association of brachycephaly with a retrotransposon that disrupts SMOC2 splicing The SMOC2 locus explains up to 36% of face length variation in dogs
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Affiliation(s)
- Thomas W Marchant
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Edward J Johnson
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Lynn McTeir
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Craig I Johnson
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Adam Gow
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Tiziana Liuti
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Dana Kuehn
- Friendship Hospital for Animals, Washington, DC 20016, USA
| | | | - Mairead L Bermingham
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | | | - Marc Nussbaumer
- Naturhistorisches Museum, Bernastrasse 15, 3005 Bern, Switzerland
| | - Megan G Davey
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - David J Argyle
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Roger M Powell
- Powell Torrance Diagnostic Services, Manor Farm Business Park, Higham Gobion, Hertfordshire SG5 3HR, UK
| | - Sérgio Guilherme
- Davies Veterinary Specialists, Manor Farm Business Park, Higham Gobion, Hertfordshire SG5 3HR, UK
| | - Johann Lang
- Division of Clinical Radiology, Department of Clinical Veterinary Medicine, University of Bern, 3001 Bern, Switzerland
| | - Gert Ter Haar
- Department of Clinical Sciences and Services, Royal Veterinary College, Hertfordshire AL9 7TA, UK
| | - Tosso Leeb
- Institute of Genetics, University of Bern, 3001 Bern, Switzerland
| | - Tobias Schwarz
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Richard J Mellanby
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Dylan N Clements
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Jeffrey J Schoenebeck
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK.
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33
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Fujita A, Isidor B, Piloquet H, Corre P, Okamoto N, Nakashima M, Tsurusaki Y, Saitsu H, Miyake N, Matsumoto N. De novo MEIS2 mutation causes syndromic developmental delay with persistent gastro-esophageal reflux. J Hum Genet 2016; 61:835-8. [DOI: 10.1038/jhg.2016.54] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 04/13/2016] [Accepted: 04/17/2016] [Indexed: 11/09/2022]
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34
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Quantitative trait locus analysis of body shape divergence in nine-spined sticklebacks based on high-density SNP-panel. Sci Rep 2016; 6:26632. [PMID: 27226078 PMCID: PMC4880927 DOI: 10.1038/srep26632] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 05/06/2016] [Indexed: 12/26/2022] Open
Abstract
Heritable phenotypic differences between populations, caused by the selective effects of distinct environmental conditions, are of commonplace occurrence in nature. However, the actual genomic targets of this kind of selection are still poorly understood. We conducted a quantitative trait locus (QTL) mapping study to identify genomic regions responsible for morphometric differentiation between genetically and phenotypically divergent marine and freshwater nine-spined stickleback (Pungitius pungitius) populations. Using a dense panel of SNP-markers obtained by restriction site associated DNA sequencing of an F2 recombinant cross, we found 22 QTL that explained 3.5-12.9% of phenotypic variance in the traits under investigation. We detected one fairly large-effect (PVE = 9.6%) QTL for caudal peduncle length-a trait with a well-established adaptive function showing clear differentiation among marine and freshwater populations. We also identified two large-effect QTL for lateral plate numbers, which are different from the lateral plate QTL reported in earlier studies of this and related species. Hence, apart from identifying several large-effect QTL in shape traits showing adaptive differentiation in response to different environmental conditions, the results suggest intra- and interspecific heterogeneity in the genomic basis of lateral plate number variation.
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35
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From vestigial to vestigial-like: the Drosophila gene that has taken wing. Dev Genes Evol 2016; 226:297-315. [DOI: 10.1007/s00427-016-0546-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 04/10/2016] [Indexed: 12/16/2022]
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36
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Davis A, Reubens MC, Stellwag EJ. Functional and Comparative Genomics of Hoxa2 Gene cis-Regulatory Elements: Evidence for Evolutionary Modification of Ancestral Core Element Activity. J Dev Biol 2016; 4:jdb4020015. [PMID: 29615583 PMCID: PMC5831782 DOI: 10.3390/jdb4020015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 03/15/2016] [Accepted: 03/17/2016] [Indexed: 11/24/2022] Open
Abstract
Hoxa2 is an evolutionarily conserved developmental regulatory gene that functions to specify rhombomere (r) and pharyngeal arch (PA) identities throughout the Osteichthyes. Japanese medaka (Oryzias latipes) hoxa2a, like orthologous Hoxa2 genes from other osteichthyans, is expressed during embryogenesis in r2–7 and PA2-7, whereas the paralogous medaka pseudogene, ψhoxa2b, is expressed in noncanonical Hoxa2 domains, including the pectoral fin buds. To understand the evolution of cis-regulatory element (CRE) control of gene expression, we conducted eGFP reporter gene expression studies with extensive functional mapping of several conserved CREs upstream of medaka hoxa2a and ψhoxa2b in transient and stable-line transgenic medaka embryos. The CREs tested were previously shown to contribute to directing mouse Hoxa2 gene expression in r3, r5, and PA2-4. Our results reveal the presence of sequence elements embedded in the medaka hoxa2a and ψhoxa2b upstream enhancer regions (UERs) that mediate expression in r4 and the PAs (hoxa2a r4/CNCC element) or in r3–7 and the PAs ψhoxa2b r3–7/CNCC element), respectively. Further, these elements were shown to be highly conserved among osteichthyans, which suggests that the r4 specifying element embedded in the UER of Hoxa2 is a deeply rooted rhombomere specifying element and the activity of this element has been modified by the evolution of flanking sequences that redirect its activity to alternative developmental compartments.
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Affiliation(s)
- Adam Davis
- Department of Biology and Physical Sciences, Gordon State College, Barnesville, GA 30204, USA.
| | - Michael C Reubens
- The Scripps Research Institute, 10550 N, Torrey Pines Road, MB3, La Jolla, CA 92037, USA.
| | - Edmund J Stellwag
- Department of Biology, Howell Science Complex, East Carolina University, Greenville, NC 27858, USA.
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37
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Ding Y, Colozza G, Zhang K, Moriyama Y, Ploper D, Sosa EA, Benitez MDJ, De Robertis EM. Genome-wide analysis of dorsal and ventral transcriptomes of the Xenopus laevis gastrula. Dev Biol 2016; 426:176-187. [PMID: 27016259 PMCID: PMC5033668 DOI: 10.1016/j.ydbio.2016.02.032] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 01/14/2016] [Accepted: 02/26/2016] [Indexed: 12/31/2022]
Abstract
RNA sequencing has allowed high-throughput screening of differential gene expression in many tissues and organisms. Xenopus laevis is a classical embryological and cell-free extract model system, but its genomic sequence had been lacking due to difficulties arising from allotetraploidy. There is currently much excitement surrounding the release of the completed X. laevis genome (version 9.1) by the Joint Genome Institute (JGI), which provides a platform for genome-wide studies. Here we present a deep RNA-seq dataset of transcripts expressed in dorsal and ventral lips of the early Xenopus gastrula embryo using the new genomic information, which was further annotated by blast searches against the human proteome. Overall, our findings confirm previous results from differential screenings using other methods that uncovered classical dorsal genes such as Chordin, Noggin and Cerberus, as well as ventral genes such as Sizzled, Ventx, Wnt8 and Bambi. Complete transcriptome-wide tables of mRNAs suitable for data mining are presented, which include many novel dorsal- and ventral-specific genes. RNA-seq was very quantitative and reproducible, and allowed us to define dorsal and ventral signatures useful for gene set expression analyses (GSEA). As an example of a new gene, we present here data on an organizer-specific secreted protein tyrosine kinase known as Pkdcc (protein kinase domain containing, cytoplasmic) or Vlk (vertebrate lonesome kinase). Overexpression experiments indicate that Pkdcc can act as a negative regulator of Wnt/ β-catenin signaling independently of its kinase activity. We conclude that RNA-Seq in combination with the X. laevis complete genome now available provides a powerful tool for unraveling cell-cell signaling pathways during embryonic induction.
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Affiliation(s)
- Yi Ding
- Howard Hughes Medical Institute and Department of Biological Chemistry, University of California, Los Angeles, CA 90095-1662, USA
| | - Gabriele Colozza
- Howard Hughes Medical Institute and Department of Biological Chemistry, University of California, Los Angeles, CA 90095-1662, USA
| | - Kelvin Zhang
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, USA
| | - Yuki Moriyama
- Howard Hughes Medical Institute and Department of Biological Chemistry, University of California, Los Angeles, CA 90095-1662, USA
| | - Diego Ploper
- Howard Hughes Medical Institute and Department of Biological Chemistry, University of California, Los Angeles, CA 90095-1662, USA
| | - Eric A Sosa
- Howard Hughes Medical Institute and Department of Biological Chemistry, University of California, Los Angeles, CA 90095-1662, USA
| | - Maria D J Benitez
- Howard Hughes Medical Institute and Department of Biological Chemistry, University of California, Los Angeles, CA 90095-1662, USA
| | - Edward M De Robertis
- Howard Hughes Medical Institute and Department of Biological Chemistry, University of California, Los Angeles, CA 90095-1662, USA.
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Van Otterloo E, Williams T, Artinger KB. The old and new face of craniofacial research: How animal models inform human craniofacial genetic and clinical data. Dev Biol 2016; 415:171-187. [PMID: 26808208 DOI: 10.1016/j.ydbio.2016.01.017] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 01/16/2016] [Accepted: 01/21/2016] [Indexed: 12/31/2022]
Abstract
The craniofacial skeletal structures that comprise the human head develop from multiple tissues that converge to form the bones and cartilage of the face. Because of their complex development and morphogenesis, many human birth defects arise due to disruptions in these cellular populations. Thus, determining how these structures normally develop is vital if we are to gain a deeper understanding of craniofacial birth defects and devise treatment and prevention options. In this review, we will focus on how animal model systems have been used historically and in an ongoing context to enhance our understanding of human craniofacial development. We do this by first highlighting "animal to man" approaches; that is, how animal models are being utilized to understand fundamental mechanisms of craniofacial development. We discuss emerging technologies, including high throughput sequencing and genome editing, and new animal repository resources, and how their application can revolutionize the future of animal models in craniofacial research. Secondly, we highlight "man to animal" approaches, including the current use of animal models to test the function of candidate human disease variants. Specifically, we outline a common workflow deployed after discovery of a potentially disease causing variant based on a select set of recent examples in which human mutations are investigated in vivo using animal models. Collectively, these topics will provide a pipeline for the use of animal models in understanding human craniofacial development and disease for clinical geneticist and basic researchers alike.
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Affiliation(s)
- Eric Van Otterloo
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
| | - Trevor Williams
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kristin Bruk Artinger
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
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Lemos C, Hardt MS, Juneja M, Voss C, Förster S, Jerchow B, Haider W, Bläker H, Stein U. MACC1 Induces Tumor Progression in Transgenic Mice and Colorectal Cancer Patients via Increased Pluripotency Markers Nanog and Oct4. Clin Cancer Res 2016; 22:2812-24. [PMID: 26758557 DOI: 10.1158/1078-0432.ccr-15-1425] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 12/03/2015] [Indexed: 11/16/2022]
Abstract
PURPOSE We have previously identified the gene MACC1 as a strong prognostic biomarker for colorectal cancer metastasis and patient survival. Here, we report for the first time the generation of transgenic mouse models for MACC1. EXPERIMENTAL DESIGN We generated mice with transgenic overexpression of MACC1 in the intestine driven by the villin promoter (vil-MACC1) and crossed them with Apc(Min) mice (vil-MACC1/Apc(Min)). RESULTS vil-MACC1/Apc(Min) mice significantly increased the total number of tumors (P = 0.0056). This was particularly apparent in large tumors (≥3-mm diameter; P = 0.0024). A detailed histopathologic analysis of these lesions demonstrated that the tumors from the vil-MACC1/Apc(Min) mice had a more invasive phenotype and, consequently, showed a significantly reduced survival time than Apc(Min) mice (P = 0.03). Molecular analysis revealed an increased Wnt and pluripotency signaling in the tumors of vil-MACC1/Apc(Min) mice. Specifically, we observed a prominent upregulation of the pluripotency markers Oct4 and Nanog in these tumors compared with Apc(Min) controls. Finally, we could also validate that Oct4 and Nanog are regulated by MACC1 in vitro and strongly correlate with MACC1 levels in a cohort of 60 tumors of colorectal cancer patients (r = 0.7005 and r = 0.6808, respectively; P > 0.0001 and P > 0.0002, respectively). CONCLUSIONS We provide proof of principle that MACC1-induced tumor progression in colorectal cancer acts, at least in part, via the newly discovered MACC1/Nanog/Oct4 axis. These findings might have important implications for the design of novel therapeutic intervention strategies to restrict tumor progression. Clin Cancer Res; 22(11); 2812-24. ©2016 AACR.
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Affiliation(s)
- Clara Lemos
- Experimental and Clinical Research Center, a joint cooperation between the Charité Medical Faculty and the Max-Delbrück-Center for Molecular Medicine, Berlin, Germany.
| | - Markus S Hardt
- Experimental and Clinical Research Center, a joint cooperation between the Charité Medical Faculty and the Max-Delbrück-Center for Molecular Medicine, Berlin, Germany. German Cancer Consortium, Heidelberg, Germany
| | - Manisha Juneja
- Experimental and Clinical Research Center, a joint cooperation between the Charité Medical Faculty and the Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Cynthia Voss
- Experimental and Clinical Research Center, a joint cooperation between the Charité Medical Faculty and the Max-Delbrück-Center for Molecular Medicine, Berlin, Germany. German Cancer Consortium, Heidelberg, Germany
| | - Susann Förster
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Boris Jerchow
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | | | - Hendrik Bläker
- Institute of Pathology, Charité Medical Faculty, Berlin, Germany
| | - Ulrike Stein
- Experimental and Clinical Research Center, a joint cooperation between the Charité Medical Faculty and the Max-Delbrück-Center for Molecular Medicine, Berlin, Germany. German Cancer Consortium, Heidelberg, Germany.
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Abstract
Approximately 50% of all congenital anomalies cannot be linked to any specific genetic etiology, but in recent years cost effective high throughput sequencing has emerged as an efficient strategy for identifying single nucleotide polymorphisms (SNPs) associated with disease. However, in many cases there is not enough evidence to determine if these SNPs underlie disease. To bridge this gap in our understanding advances in functional analyses are warranted. Several preclinical model systems are currently being utilized to provide such evidence, including the advantageous zebrafish embryo. While every system exhibits disadvantages and caveats, a new era of multidisciplinary research has evolved, which uses a broad spectrum of functional analysis tools. This approach will make it possible to identify potential therapeutic targets for both common and rare human disorders.
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Affiliation(s)
- Anita M Quintana
- Department of Biological Sciences, The University of Texas at El Paso, 500 West University Avenue, El Paso TX 79934
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41
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Machon O, Masek J, Machonova O, Krauss S, Kozmik Z. Meis2 is essential for cranial and cardiac neural crest development. BMC DEVELOPMENTAL BIOLOGY 2015; 15:40. [PMID: 26545946 PMCID: PMC4636814 DOI: 10.1186/s12861-015-0093-6] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 11/03/2015] [Indexed: 11/28/2022]
Abstract
Background TALE-class homeodomain transcription factors Meis and Pbx play important roles in formation of the embryonic brain, eye, heart, cartilage or hematopoiesis. Loss-of-function studies of Pbx1, 2 and 3 and Meis1 documented specific functions in embryogenesis, however, functional studies of Meis2 in mouse are still missing. We have generated a conditional allele of Meis2 in mice and shown that systemic inactivation of the Meis2 gene results in lethality by the embryonic day 14 that is accompanied with hemorrhaging. Results We show that neural crest cells express Meis2 and Meis2-defficient embryos display defects in tissues that are derived from the neural crest, such as an abnormal heart outflow tract with the persistent truncus arteriosus and abnormal cranial nerves. The importance of Meis2 for neural crest cells is further confirmed by means of conditional inactivation of Meis2 using crest-specific AP2α-IRES-Cre mouse. Conditional mutants display perturbed development of the craniofacial skeleton with severe anomalies in cranial bones and cartilages, heart and cranial nerve abnormalities. Conclusions Meis2-null mice are embryonic lethal. Our results reveal a critical role of Meis2 during cranial and cardiac neural crest cells development in mouse. Electronic supplementary material The online version of this article (doi:10.1186/s12861-015-0093-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ondrej Machon
- Institute of Molecular Genetics, The Czech Academy of Sciences, 14200, Praha, Czech Republic.
| | - Jan Masek
- Institute of Molecular Genetics, The Czech Academy of Sciences, 14200, Praha, Czech Republic.
| | - Olga Machonova
- Institute of Molecular Genetics, The Czech Academy of Sciences, 14200, Praha, Czech Republic.
| | - Stefan Krauss
- Unit for Cell Signaling, Oslo University Hospital, N-0349, Oslo, Norway.
| | - Zbynek Kozmik
- Institute of Molecular Genetics, The Czech Academy of Sciences, 14200, Praha, Czech Republic.
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42
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Uribe RA, Bronner ME. Meis3 is required for neural crest invasion of the gut during zebrafish enteric nervous system development. Mol Biol Cell 2015; 26:3728-40. [PMID: 26354419 PMCID: PMC4626059 DOI: 10.1091/mbc.e15-02-0112] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 09/02/2015] [Indexed: 01/02/2023] Open
Abstract
Loss of Meis3 leads to defects in enteric neural crest cell migration, number, and proliferation during colonization of the gut. This leads to colonic aganglionosis, in which the hindgut is devoid of neurons, identifying it as a novel candidate factor in the etiology of Hirschsprung’s disease during enteric nervous system development. During development, vagal neural crest cells fated to contribute to the enteric nervous system migrate ventrally away from the neural tube toward and along the primitive gut. The molecular mechanisms that regulate their early migration en route to and entry into the gut remain elusive. Here we show that the transcription factor meis3 is expressed along vagal neural crest pathways. Meis3 loss of function results in a reduction in migration efficiency, cell number, and the mitotic activity of neural crest cells in the vicinity of the gut but has no effect on neural crest or gut specification. Later, during enteric nervous system differentiation, Meis3-depleted embryos exhibit colonic aganglionosis, a disorder in which the hindgut is devoid of neurons. Accordingly, the expression of Shh pathway components, previously shown to have a role in the etiology of Hirschsprung’s disease, was misregulated within the gut after loss of Meis3. Taken together, these findings support a model in which Meis3 is required for neural crest proliferation, migration into, and colonization of the gut such that its loss leads to severe defects in enteric nervous system development.
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Affiliation(s)
- Rosa A Uribe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Marianne E Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
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Hoxa2 selectively enhances Meis binding to change a branchial arch ground state. Dev Cell 2015; 32:265-77. [PMID: 25640223 PMCID: PMC4333904 DOI: 10.1016/j.devcel.2014.12.024] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 07/18/2014] [Accepted: 12/23/2014] [Indexed: 02/07/2023]
Abstract
Hox transcription factors (TFs) are essential for vertebrate development, but how these evolutionary conserved proteins function in vivo remains unclear. Because Hox proteins have notoriously low binding specificity, they are believed to bind with cofactors, mainly homeodomain TFs Pbx and Meis, to select their specific targets. We mapped binding of Meis, Pbx, and Hoxa2 in the branchial arches, a series of segments in the developing vertebrate head. Meis occupancy is largely similar in Hox-positive and -negative arches. Hoxa2, which specifies second arch (IIBA) identity, recognizes a subset of Meis prebound sites that contain Hox motifs. Importantly, at these sites Meis binding is strongly increased. This enhanced Meis binding coincides with active enhancers, which are linked to genes highly expressed in the IIBA and regulated by Hoxa2. These findings show that Hoxa2 operates as a tissue-specific cofactor, enhancing Meis binding to specific sites that provide the IIBA with its anatomical identity. Meis provides a ground state that is common to all the branchial arches Hoxa2 recognizes Meis prebound sites in the second arch that contain Hox motifs Hoxa2 enhances Meis binding, which coincides with active enhancers, at these sites Hoxa2 modulates the ground-state binding of Meis to instruct second arch identity
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44
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Pietri JE, Cheung KW, Luckhart S. Knockdown of mitogen-activated protein kinase (MAPK) signalling in the midgut of Anopheles stephensi mosquitoes using antisense morpholinos. INSECT MOLECULAR BIOLOGY 2014; 23:558-65. [PMID: 24866718 PMCID: PMC4159403 DOI: 10.1111/imb.12103] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Arthropod-borne infectious diseases are responsible for nearly 1.5 million deaths annually across the globe, with malaria responsible for >50% of these deaths. Recent efforts to enhance malaria control have focused on developing genetically modified Anopheles mosquitoes that are resistant to malaria parasite infection by manipulating proteins that are essential to the immune response. Although this approach has shown promise, the lack of efficient genetic tools in the mosquito makes it difficult to investigate innate immunity using reverse genetics. Current gene knockdown strategies based on small interfering RNA are typically labourious, inefficient, and require extensive training. In the present study, we describe the use of morpholino antisense oligomers to knockdown MEK-ERK signalling in the midgut of Anopheles stephensi through a simple feeding protocol. Anti-MEK morpholino provided in a saline meal was readily ingested by female mosquitoes with minimal toxicity and resulted in knockdown of total MEK protein levels 3-4 days after morpholino feeding. Further, anti-MEK morpholino feeding attenuated inducible phosphorylation of the downstream kinase ERK and, as predicted by previous work, reduced parasite burden in mosquitoes infected with Plasmodium falciparum. To our knowledge, this is the first example of morpholino use for target protein knockdown via feeding in an insect vector. Our results suggest this method is not only efficient for studies of individual proteins, but also for studies of phenotypic control by complex cell signalling networks. As such, our protocol is an effective alternative to current methods for gene knockdown in arthropods.
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Affiliation(s)
- Jose E. Pietri
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616
| | - Kong W. Cheung
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616
| | - Shirley Luckhart
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616
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Bordoli MR, Yum J, Breitkopf SB, Thon JN, Italiano JE, Xiao J, Worby C, Wong SK, Lin G, Edenius M, Keller TL, Asara JM, Dixon JE, Yeo CY, Whitman M. A secreted tyrosine kinase acts in the extracellular environment. Cell 2014; 158:1033-1044. [PMID: 25171405 PMCID: PMC4149754 DOI: 10.1016/j.cell.2014.06.048] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 05/06/2014] [Accepted: 06/20/2014] [Indexed: 11/17/2022]
Abstract
Although tyrosine phosphorylation of extracellular proteins has been reported to occur extensively in vivo, no secreted protein tyrosine kinase has been identified. As a result, investigation of the potential role of extracellular tyrosine phosphorylation in physiological and pathological tissue regulation has not been possible. Here, we show that VLK, a putative protein kinase previously shown to be essential in embryonic development, is a secreted protein kinase, with preference for tyrosine, that phosphorylates a broad range of secreted and ER-resident substrate proteins. We find that VLK is rapidly and quantitatively secreted from platelets in response to stimuli and can tyrosine phosphorylate coreleased proteins utilizing endogenous as well as exogenous ATP sources. We propose that discovery of VLK activity provides an explanation for the extensive and conserved pattern of extracellular tyrosine phosphophorylation seen in vivo, and extends the importance of regulated tyrosine phosphorylation into the extracellular environment.
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Affiliation(s)
- Mattia R Bordoli
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - Jina Yum
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA; Department of Life Science and Global Top5 Research Program, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Susanne B Breitkopf
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Jonathan N Thon
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Joseph E Italiano
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Vascular Biology Program, Department of Surgery, Children's Hospital, Boston, MA 02115, USA
| | - Junyu Xiao
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92031, USA
| | - Carolyn Worby
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92031, USA
| | - Swee-Kee Wong
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - Grace Lin
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - Maja Edenius
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - Tracy L Keller
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - John M Asara
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Jack E Dixon
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92031, USA
| | - Chang-Yeol Yeo
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA; Department of Life Science and Global Top5 Research Program, Ewha Womans University, Seoul 120-750, Republic of Korea.
| | - Malcolm Whitman
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA.
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Mommaerts H, Esguerra CV, Hartmann U, Luyten FP, Tylzanowski P. Smoc2 modulates embryonic myelopoiesis during zebrafish development. Dev Dyn 2014; 243:1375-90. [PMID: 25044883 DOI: 10.1002/dvdy.24164] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 06/14/2014] [Accepted: 07/02/2014] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND SMOC2 is a member of the BM-40 (SPARC) family of matricellular proteins, reported to influence signaling in the extracellular compartment. In mice, Smoc2 is expressed in many different tissues and was shown to enhance the response to angiogenic growth factors, mediate cell adhesion, keratinocyte migration, and metastasis. Additionally, SMOC2 is associated with vitiligo and craniofacial and dental defects. The function of Smoc2 during early zebrafish development has not been determined to date. RESULTS In pregastrula zebrafish embryos, smoc2 is expressed ubiquitously. As development progresses, the expression pattern becomes more anteriorly restricted. At the onset of blood cell circulation, smoc2 morphants presented a mild ventralization of posterior structures. Molecular analysis of the smoc2 morphants indicated myelopoietic defects in the rostral blood islands during segmentation stages. Hemangioblast development and further specification of the myeloid progenitor cells were shown to be impaired. Additional experiments indicated that Bmp target genes were down-regulated in smoc2 morphants. CONCLUSIONS Our findings reveal that Smoc2 is an essential player in the development of myeloid cells of the anterior lateral plate mesoderm during embryonic zebrafish development. Furthermore, our data show that Smoc2 affects the transcription of Bmp target genes without affecting initial dorsoventral patterning or mesoderm development.
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Affiliation(s)
- Hendrik Mommaerts
- Laboratory for Developmental and Stem Cell Biology, Skeletal Biology and Engineering Research Center, Department of Development and Regeneration, KU Leuven - University of Leuven, Leuven, Belgium
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